How calculate standard deviation of ADC histogram for rms noise analysis?
The standard deviation is calculated on the set of output codes recorded at the output of the ADC.  If you have the data in time sequence as is was captured, you can calculate the standard deviation directly from that data set. If the data has already been converted to histogram form, as you describe above, you will need to enter each output  code value into your data set as many times as the counts that are in its histogram bin.

For example, if code 127 had 3 hits, code 128 had 7 hits, and code 129 had 4 hits, you would enter this into the online calculator: 

127, 127, 127, 128, 128, 128, 128, 128, 128, 128, 129, 129, 129, 129  

(your data set should be much larger of course)