ding-lab/CharGer issues and pull requests

#58 - Misinformation in README and Python version conflict

Issue - State: open - Opened by altundal19 3 months ago

#57 - Unable to install charger via pip or conda

Issue - State: open - Opened by abhayr20 about 1 year ago

#56 - Default inheritance table and gene list for BP2 and PP1.

Issue - State: open - Opened by yangyxt about 2 years ago

#55 - PM5 found 0 pathogenic variants

Issue - State: open - Opened by lihm1 over 2 years ago

#54 - Need most updated ClinVar files

Issue - State: open - Opened by TimmPKU about 3 years ago

#53 - is this software alive?

Issue - State: open - Opened by thedam over 3 years ago

#52 - NameError: global name 'entrezaip' is not defined when doing clinvar search

Issue - State: open - Opened by mingoo426 almost 4 years ago

#51 - Install error

Issue - State: closed - Opened by mingoo426 almost 4 years ago

#50 - CharGer::runIndelModules Error:

Issue - State: open - Opened by rescuz about 4 years ago

#49 - What Cross-reference data files to use and where to get for lung cancer

Issue - State: open - Opened by JiaweiDai-create about 4 years ago

#48 - Reference for inheritanceGeneList 20160301_Rahman_KJ_KH_gene_table_CharGer.txt.gz

Issue - State: closed - Opened by nah2025 over 4 years ago - 2 comments

#47 - error: Hint: is the input amino acid change column correct , charger version 0.5.4

Issue - State: closed - Opened by nah2025 over 4 years ago - 1 comment

#46 - installed Charger 0.5.4 but version in help is 0.5.3

Issue - State: closed - Opened by nah2025 over 4 years ago - 1 comment

#45 - Null Variant classified as Benign

Issue - State: closed - Opened by NTNguyen13 over 4 years ago - 3 comments

#44 - Provide instructions to generate the HotSpot3D cluster file

Issue - State: open - Opened by ccwang002 over 4 years ago

#43 - IndexError: list index out of range while running with Mac-Clinvar

Issue - State: closed - Opened by NTNguyen13 over 4 years ago - 4 comments

#42 - Problems to run CharGer v0.5.4

Issue - State: closed - Opened by yubau1112 over 4 years ago - 5 comments

#41 - I can not get any output file using v0.6.0b1 version

Issue - State: closed - Opened by yubau1112 over 4 years ago - 1 comment

#40 - can you give me an example command with run VEP?

Issue - State: closed - Opened by yubau1112 almost 5 years ago - 4 comments

#39 - run demo.sh, report error

Issue - State: closed - Opened by xuanzhu1213 almost 5 years ago - 2 comments

#38 - something wrong

Issue - State: closed - Opened by yubau1112 almost 5 years ago - 7 comments

#37 - All variants classified as Benign or Uncertain Significance

Issue - State: closed - Opened by nrosewick about 5 years ago - 4 comments

#36 - biomine warning

Issue - State: closed - Opened by rescuz about 5 years ago - 3 comments

#35 - V0.5.4

Pull Request - State: closed - Opened by fernanda-rodrigues about 5 years ago

#34 - V.0.5.3

Pull Request - State: closed - Opened by fernanda-rodrigues about 5 years ago

#33 - Even VEP90 branch with master branch

Pull Request - State: closed - Opened by fernanda-rodrigues about 5 years ago

#32 - -o output read as input?

Issue - State: closed - Opened by laura-budurlean about 5 years ago

#31 - Fix HGVSc parsing from VEP annotation

Pull Request - State: closed - Opened by fernanda-rodrigues over 5 years ago

#30 - can't input maf.file

Issue - State: closed - Opened by rescuz over 5 years ago - 2 comments
Labels: help wanted

#29 - I couldn't find demo/runDemo.sh /pathogenicVariants.vcf

Issue - State: closed - Opened by rescuz over 5 years ago - 1 comment

#28 - getExAC_MAF not behaving like expected

Pull Request - State: closed - Opened by mmoisse over 5 years ago

#27 - Fixed mismatch in getRefAltAminoAcids

Pull Request - State: closed - Opened by mmoisse over 5 years ago

#26 - PS1 is samePeptideChange

Pull Request - State: closed - Opened by mmoisse over 5 years ago

#25 - isConflicted only if path and bening

Pull Request - State: closed - Opened by mmoisse over 5 years ago - 1 comment

#24 - re.match is not working like intended

Pull Request - State: closed - Opened by mmoisse over 5 years ago - 2 comments

#23 - clinical_significance_ordered is better

Pull Request - State: closed - Opened by mmoisse over 5 years ago

#22 - Fix: always Likely benign and Likely pathogenic

Pull Request - State: closed - Opened by mmoisse over 5 years ago

#21 - clinvarDone always true

Issue - State: closed - Opened by mmoisse over 5 years ago - 1 comment
Labels: question

#20 - I used CharGer. But I got different results.

Issue - State: closed - Opened by oghzzang over 5 years ago - 2 comments

#19 - Fix bug

Pull Request - State: closed - Opened by icebert over 5 years ago - 3 comments

#18 - All Uncertain Significance

Issue - State: closed - Opened by ekofman over 5 years ago - 1 comment
Labels: help wanted

#17 - could not find amino acid change or intronic change

Issue - State: closed - Opened by HeXY0515 almost 6 years ago - 2 comments
Labels: BioMine-related-issue