Conversation
ecoli db reference files updated to match aligner switch
For readability, the .gitignore file was reduced using wildcard characters
Add support for hg38 and expanded cell lines on StrainID -add hg38_VCF db with similar cell lines to hg19_VCF -add hg38_ENCODE db with ENCODE cell lines at least 250 variants big -add scripts and refs for building full hg38_DepMap db -update README to describe how Model.csv was downloaded. -minor fix to generate_sacCer3_VariantDB.sh usage typo -.gitignore updated appropriately
the presence of this script implies validation was performed on mm10. Removing now to avoid confusion for future users
add scripts to generate hg38 versions of the HELA and K562 datasets at 20M
missed some files in the reference DBs when I switched from bowtie2 to bwa for the aligner
create a second version 2 of the database with an expanded set of epitope sequences
-update README with more details about script execution -add gzipped parsed text file results -update gitignore with fixes to ENCODE StrainID directory typos -change results parsing script to use pandas and include every Cell Line score instead of just the best one
update script for parsing and building violin plots from ENCODE StrainID results. Add option to filter by various assays and include README lines and some highlighted violin PNG figures
Our the ID scripts have long been refactored to use Python3 over Python2 but the usage was not fixed to reflect this. This commit fixes the usage statement
For Supplementary figure 2 and supplementary table 11, we pulled 100 ENCODE datasets and ran StrainID on them using the full hg38_DepMap reference to build at table and histogram of StrainID scores showing that "correct" strainid scores show good separation from "incorrect" ones.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Update code base with more scripts and simulations responding to reviewer comments