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49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 6/22/2012 [Script] Absolute Risk Reduction This script calculates the reduced risk for each genotype given binary disease status and treatment status columns. The script requires a spreadsheet that contains at least two binary columns and several genotypic columns. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 6/21/2012 [Script] Convert Dosages to Genotypes This script converts allelic dosage values to genotypes based on user-specified thresholds. The dosage data may be in Single- or Double-Dosage format and may have samples in the row labels or column headers. If the samples are in the column headers, the spreadsheet may contain map information and allele translation values. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Edit | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 5/17/2013 [Script] Quantile Transformation This script categorizes a numeric column into N user-specified quantiles. The cutoff points are calculated over all non-missing values and column values are compared against these cutoffs with <=. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Edit | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 6/20/2012 [Script] Calculate Pseudo Lambda This script calculates a pseudo-lambda value on a column containing p-values. The formula used to calculate the pseudo lambda value is as follows: More info » [Author] Autumn Laughbaum Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 6/15/2012 [Script] Correct P-Values for Multiple Tests This script takes a column of p-values and outputs several multiple testing corrections including Bonferroni, FDR (Storey 2002), BH FDR (Benjamini-Hochburg 1995) and BY FDR (Benjamini-Yekutieli 2001). More info » [Author] Greta Peterson Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 5/31/2012 [Script] Move Columns to Location This script moves all columns of a user-specified type to the user-specified location (Beginning or End). This will allow the user to group all columns of the same type together. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Edit | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 5/3/2012 [Script] Chi-Squared Test with Continuity Correction This script performs a Chi-squared test on a spreadsheet with a binary dependent and genotypic data. The output will contain results for the traditional test as well as results with the Yates continuity correction applied. The following genetic models are available; Basic Allelic, Dominant, or Recessive. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 11/10/2011 [Script] Inactivate Duplicate Column Headers This script scans a spreadsheet's column headers and inactivates all additional occurrences of a column header (only the first occurrence remains active). More info » [Author] Greta Peterson Golden Helix [Category] | Filter | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 2/28/2012 [Script] Import Merlin PED DAT This import script imports PED/DAT files created in MERLIN. File delimiters may be comma, whitespace or tab and allele delimiters may be whitespace or /. The data may include several phenotype, covariate and genotype columns. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Import | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 2/10/2012 [Script] MAF Filtering on Recoded Spreadsheet This script calculates minor allele frequency (MAF) on recoded data created by Recode Genotypes with X Chromosome Adjustment. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Filter | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 2/10/2012 [Script] Recode Genotypes with X Chromosome Adjustment This script recodes genotypes based on an additive model with major/minor allele classification. Markers within the selected chromosomes are adjusted for male samples. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Recode | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 2/7/2012 [Script] Import Tall Skinny Format This import script is designed to import genotypic data that is stored in a tall skinny format. The user will specify the variant name column, sample name column, and data column(s). More info » [Author] Autumn Laughbaum Golden Helix [Category] | Import | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 2/3/2012 [Script] Filter Columns by Regular Expression This script takes a regular expression and activates all columns which contain an expression match in the column header. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Filter | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 3/20/2015 [Script] Rename Genotypes This script scans the genotypic columns to find all existing genotypes, and then prompts for replacements. The resulting spreadsheet has the same dimensions with the appropriate genotype substitutions. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Edit | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/30/2012 [Script] Create Column From Row Labels This script allows the user to add the row labels as a column in the spreadsheet. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Edit | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/25/2012 [Script] Average Markers by Gene This script calculates an average value for each row over each region as defined by a gene annotation track or a string marker map field. This script requires a marker mapped spreadsheet with several quantitative columns. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 11/10/2011 [Script] Convert Binary and Integer Values to Genotypes This script recodes binary and integer genotypes to the standard genotype format of A_A, A_B, and B_B. Prompts for value of A_A, A_B, and B_B. All other numbers are encoded as missing. Thus if there is multi-allelic data in the spreadsheet, all numbers other than those specified will be encoded as "?". More info » [Author] Greta Linse Peterson Golden Helix [Category] | Edit | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 11/10/2011 [Script] Create Pseudo Marker Mapped Spreadsheet From a non-marker mapped spreadsheet this script creates a new marker mapped spreadsheet with a pseudo marker map containing chromosome 1, positions 1 - #Rows. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 11/10/2011 [Script] Create Spreadsheet for Segmentation Based on a column from a spreadsheet, this script creates a new spreadsheet with a pseudo marker map and generic column headers making it suitable for running CNAM optimal segmenting. More info » [Author] Greta Linse Peterson Golden Helix [Category] | CNV Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 11/10/2011 [Script] Frequency Table This script will calculate the frequency distribution of two columns in a spreadsheet. The script can be accessed through the scripts menu and will prompt the user to select two non-real columns. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 11/10/2011 [Script] Split Column on Specified Delimiter This script prompts the user to select a column that needs to be split on a specified delimiter and for the delimiter to use. The delimiter can be more than one character. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Edit | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 11/10/2011 [Script] Genetic Distance between Samples This script is designed to calculate Cochran-Mantel-Haenszel statistics, given several different spreadsheets corresponding to data from several different strata. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 11/10/2011 [Script] MIP CN Transformation This script creates 5 transposed spreadsheets, one for each column imported from the MIP Array copy number text file: Copy A, Copy B, CopyNumber, AlleleRatio, and AllelicDifference More info » [Author] Greta Linse Peterson Golden Helix [Category] | Edit | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 11/10/2011 [Script] Select Subset of Data by XY Coordinates This script takes an upper and lower bound for two numeric columns and creates a subset spreadsheet for the two columns. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Filter | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 10/25/2011 [Script] CMH Test over Several Strata This script is designed to calculate Cochran-Mantel-Haenszel statistics, given several different spreadsheets corresponding to data from several different strata. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 10/04/2011 [Script] Genotype Statistics Summary This script takes a spreadsheet that contains a case/control dependent variable and SNPs and runs all of the genotype association tests as well as tests for a heterozygous advantage model (Dd vs DD, dd) and a homozygous comparison model (DD vs dd). Also calculates Chi Squared Scores, Correlation/Trend test scores and completes count tables. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 7/28/2011 [Script] Alternate Allele Frequency This script calculates the percentage of alternate alleles over all samples for each variant. The resulting spreadsheet has columns containing the reference count, alternate allele, alternate allele frequency, reference allele count and alternate allele count. More info » [Author] Mike Thiesen Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 6/23/2011 [Script] Create Table for Significant Region Creates a spreadsheet with significant regions from a spreadsheet of p-values. This script extracts p-values more extreme than a certain significance value (cutoff) and combines the remaining markers into segments. If two markers are on different chromosomes or more than a certain distance apart (split), a new region is created. More info » [Author] Ingo Helbig UK-SH Kiel [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 6/23/2014 [Script] Extract Info from Regression Stats Viewer This script scans the Regression Statistics Viewer output and prints out the p-value after correcting for any covariates. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Regression | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 4/21/2011 [Script] Filter by Marker Map Field This function takes a map field from the current spreadsheet as input, then activates or inactivates based on a given threshold or list, or both. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Filter | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 4/21/2011 [Script] KBAC with Permutation Testing The Kernel-Based Adaptive Cluster (KBAC) method by Liu and Leal [Liu and Leal 2010] first catalogs the variant data within each of a number of regions into multi-marker genotypes. Since the variants are rare, only a relatively few different multi-marker genotypes will be found in any given region. More info » [Author] James Grover Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 4/21/2011 [Script] Apply Additional Marker Map This function will apply an additional marker map to the a currently mapped spreadsheet. The user can choose to apply the new map's data to only unmapped columns or to all columns, preferring either new marker map or old marker map information. More info » [Author] Sam Gardner Golden Helix [Category] | Marker Maps | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 4/21/2011 [Script] LD Pairwise Analysis Scripts This script outputs results from LD analysis, both the EM and CHM methods and both R² and D' values. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 4/18/2011 [Script] Highlight Values in XY Scatter Plot This script plots an XY scatter plot with additional graph items to highlight values of interest. An independent column, dependent column and sample list is needed. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Plotting | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 4/7/2011 [Script] Run Multiple Genotype Association Tests This script runs genotypic association tests on multiple dependent phenotype columns. More info » [Author] Christophe Lambert, Greta Linse Peterson Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 3/14/2011 [Script] Import PennCNV This script imports PennCNV input signal intensity files, where each file contains data for a single sample. More info » [Author] Sam Gardner Golden Helix [Category] | Import | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 3/11/2011 [Script] Append Several Spreadsheets This function allows the user to append several spreadsheets in one dialog, saving the user from having to append each spreadsheet individually. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Edit | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/21/2015 [Script] Join or Merge Several Spreadsheets This function allows the user to merge several spreadsheets in one dialog, saving the user from having to merge each spreadsheet individually. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Edit | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 12/17/2014 [Script] ANOVA with Phenotype and SNPs This function makes use of the scipy package, specifically the scipy.stats.f_oneway and scipy.stats.kruskal functions. This requires a numeric phenotype column and several genotype columns which provide the grouping structure in each test. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 3/3/2011 [Script] ANOVA on Numeric Columns This function makes use of the scipy package, specifically the scipy.stats.f_oneway and scipy.stats.kruskal functions. This requires a categorical dependent column that provides the grouping structure and several numeric columns. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 3/3/2011 [Script] Import Affymetrix CN Segment Files This script will import Affymetrix CN Segment files containing copy number segment data as outputted from Affymetrix. More info » [Author] Sam Gardner Golden Helix [Category] | Import | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 3/3/2011 [Script] Filter by SIFT Synonymous Classification This function scans a marker-mapped spreadsheet with several genotypic columns and investigates the corresponding SIFT marker map synonymous or non-synonymous classifications.This script requires the purchase of the Sequence Module to function. More info » [Author] Gabe Rudy Golden Helix [Category] | Filter | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/26/2011 [Script] Activate ATCG SNPs to flip strand or to exclude SNPs These scripts can be used to identify SNPs that have ambivalent orientation by comparing a genotype dataset with a reference dataset, such as HapMap data. More info » [Author] Joost W. Morsink and Sander W. van der Laan University Medical Center Utrecht [Category] | Edit | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/26/2011 [Script] Affymetrix B Allele Frequency Calculation Using Affymetrix CEL files as its source, this script combines quantile normalized SNP A and B probe intensities for each marker into a theta value, then calculates B-Allele Frequencies for each marker. More info » [Author] Greta Linse Peterson Golden Helix [Category] | CNV Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 12/27/2013 [Script] BEAGLE/BEAGLECALL Scripts Package These scripts are for importing and exporting files from the BEAGLE and BEAGLECALL Genetic Analysis Software Packages. More info » [Author] Various GHI Staff Golden Helix [Category] | Import/Export | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/26/2011 [Script] Calculate Expected P-value This script takes spreadsheet that contains a p-value column and calculates expected p-values for the specified column. It is also optional to export expected –log10 p-values as well. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/26/2011 [Script] Chi-Squared Contingency Table This script computes the Pearson’s Chi-Squared Statistic for a contingency table with m groups and n observations (m rows and n columns). For 2x2 tables the p-value, –log10 p-value, Bonferroni p-value and –log10 Bonferroni p-value are also computed. More info » [Author] Greta Linse Peterson Golden Helix [Category] | SNP Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/26/2011 [Script] CNV PCA Search Given a spreadsheet, prompt for a principal components spreadsheet, a lower and upper bound on the number of components and a step size. Runs association tests using each components setting, does a linear regression on the least significant 90% of the data and reports the slope of the line and a goodness of fit statistic. This script can be used in conjunction with the CNV PCA Search Tutorial. More info » [Author] Christophe Lambert Golden Helix [Category] | CNV Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/26/2011 [Script] Create Table for Significant Regions This script creates a spreadsheet with significant regions from a spreadsheet of p-values (in the first column). It also extracts p-values more extreme than a certain significance value (cutoff) and combines the remaining markers into segments. If two markers are on different chromosomes or more than a certain distance apart (split), a new region is created. More info » [Author] Ingo Helbig UK-SH Kiel [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 12/27/2013 [Script] Export MACH PED_DAT Files This script exports MACH/Merlin PED and DAT formatted files. Run this script from a pedigree spreadsheet that can contain as many phenotypes as desired. The user will be provided with the option to create one file per chromosome if a marker map is applied to the pedigree spreadsheet. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Export | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/26/2011 [Script] Log Ratio Tails This script calculates percentile values for the upper and lower tails of log ratios using two user-specified thresholds. Missing values are skipped. A log ratio call rate is returned with the results. This script may also be used to identify percentiles for real-value data other than log ratios. More info » [Author] Christophe Lambert, Bryce Christensen Golden Helix [Category] | CNV Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 8/13/2013 [Script] Nonparametric Association Tests (Binary Dependent) This function makes use of the scipy package, specifically the scipy.stats.ranksums and scipy.stats.mannwhitneyu functions. With one binary dependent column, the user can perform nonparametric association tests on all numeric columns. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 8/13/2013 [Script] Nonparametric Correlation This function makes use of the scipy package, specifically the scipy.stats.spearmanr and scipy.stats.kendalltau functions. With one numeric dependent column, the user can perform nonparametric correlation tests on all numeric columns. More info » [Author] Autumn Laughbaum Golden Helix [Category] | Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/26/2011 [Script] Row Averages with Histogram This script will create a column subset from a numeric spreadsheet, then take the row averages and create a histogram of those averages. The subset is specified with a column chooser. This function is useful for LogR spreadsheets to investigate for possible CNVs. More info » [Author] Autumn Laughbaum Golden Helix [Category] | CNV Analysis | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/26/2011 [Script] Sample Pair Mismatch This script compares genotype calls from NSP and STY files and calculates the correlation between the nearest markers in the two sets. If there is a high correlation, the NSP and STY markers correspond to the same person, otherwise there is a mismatch. More info » [Author] Christophe Lambert, Greta Linse Peterson Golden Helix [Category] | Quality Assurance | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
49ded946_SVS_Add_On_Scripts_Repository__Category | [Date Modified] 1/26/2011 [Script] SNP Cluster Plots This script creates scatter plots based on A and B allele intensities that can be split on SNP genotypes to create tri-colored cluster plots. The script will work for up to 100 SNPs at a time. More info » [Author] Greta Linse Peterson Golden Helix [Category] | Plotting | [] | SVS Add-On Scripts Repository | Category | http://goldenhelix.com/SNP_Variation/scripts/index.html | 34/1438044271733.81_20150728004431-00150-ip-10-236-191-2_105535220_2.json |
c4c40d61_mage__sejda_1_0_0_RELEASE_API__Class_Summary_Description | [Class] AbstractPdfToImageParameters [Description] | Base class for a parameter meant to convert an existing pdf source to an image of a specified type. | [] | org.sejda.model.parameter.image (sejda 1.0.0.RELEASE API) | Description | http://www.sejda.org/javadocs/org/sejda/model/parameter/image/package-summary.html | 34/1438043058631.99_20150728002418-00071-ip-10-236-191-2_714128803_1.json |
c4c40d61_mage__sejda_1_0_0_RELEASE_API__Class_Summary_Description | [Class] AbstractPdfToMultipleImageParameters [Description] | Base class for a parameter meant to convert an existing pdf source to multiple images of a specified type. | [] | org.sejda.model.parameter.image (sejda 1.0.0.RELEASE API) | Description | http://www.sejda.org/javadocs/org/sejda/model/parameter/image/package-summary.html | 34/1438043058631.99_20150728002418-00071-ip-10-236-191-2_714128803_1.json |
c4c40d61_mage__sejda_1_0_0_RELEASE_API__Class_Summary_Description | [Class] AbstractPdfToSingleImageParameters [Description] | Base class for a parameter meant to convert an existing pdf source to a single image of a specified type. | [] | org.sejda.model.parameter.image (sejda 1.0.0.RELEASE API) | Description | http://www.sejda.org/javadocs/org/sejda/model/parameter/image/package-summary.html | 34/1438043058631.99_20150728002418-00071-ip-10-236-191-2_714128803_1.json |
c4c40d61_mage__sejda_1_0_0_RELEASE_API__Class_Summary_Description | [Class] PdfToJpegParameters [Description] | Parameter meant to convert an existing pdf source to JPEG images. | [] | org.sejda.model.parameter.image (sejda 1.0.0.RELEASE API) | Description | http://www.sejda.org/javadocs/org/sejda/model/parameter/image/package-summary.html | 34/1438043058631.99_20150728002418-00071-ip-10-236-191-2_714128803_1.json |
c4c40d61_mage__sejda_1_0_0_RELEASE_API__Class_Summary_Description | [Class] PdfToMultipleTiffParameters [Description] | Parameter meant to convert an existing pdf source to multiple TIFF images. | [] | org.sejda.model.parameter.image (sejda 1.0.0.RELEASE API) | Description | http://www.sejda.org/javadocs/org/sejda/model/parameter/image/package-summary.html | 34/1438043058631.99_20150728002418-00071-ip-10-236-191-2_714128803_1.json |
c4c40d61_mage__sejda_1_0_0_RELEASE_API__Class_Summary_Description | [Class] PdfToSingleTiffParameters [Description] | Parameter meant to convert an existing pdf source to a single TIFF image with multiple pages. | [] | org.sejda.model.parameter.image (sejda 1.0.0.RELEASE API) | Description | http://www.sejda.org/javadocs/org/sejda/model/parameter/image/package-summary.html | 34/1438043058631.99_20150728002418-00071-ip-10-236-191-2_714128803_1.json |
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