zwdzwd/transvar issues and pull requests

#61 - If any existing database the stores annotations

Issue - State: open - Opened by yanrongz 5 months ago

#60 - transvar does not process hgvs expressions for inversions?

Issue - State: open - Opened by DavidTamborero 11 months ago

#59 - Problem in EnsemblDB for gene_ids with lowercase characters and no gene name

Issue - State: open - Opened by manulera about 1 year ago - 1 comment

#58 - Update for Apple M1 chips

Pull Request - State: open - Opened by TaylorRPatterson over 1 year ago

#57 - Incomplete candidate_snv_variants and candidate_mnv_variants result

Issue - State: closed - Opened by DongxueMao over 2 years ago

#56 - panno batch example

Issue - State: open - Opened by XimenaBo over 2 years ago - 1 comment

#55 - discrepancy on genomic annotation

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

#54 - http://transvar.info/transvar_user/annotations/ is not correct?

Issue - State: open - Opened by 971202 over 2 years ago - 2 comments

#53 - AttributeError: 'RefGenome' object has no attribute 'faidx_handle'

Issue - State: open - Opened by LiviaMoura over 2 years ago - 3 comments

#52 - Fix/import newest version of refseq

Pull Request - State: closed - Opened by joe-albert over 2 years ago

#51 - Cannot index against the newest version of refseq

Issue - State: closed - Opened by joe-albert almost 3 years ago

#50 - Reference files missing from server

Issue - State: open - Opened by joe-albert almost 3 years ago - 1 comment

#49 - panno mode couldn't find coordinate Ensembl transcript ID

Issue - State: open - Opened by zhouzhendiao almost 3 years ago

#48 - Deviation from HGVS recommendations

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

#47 - Does/will transvar support Windows?

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

#46 - question concerning implementation HGVS 3´ rule of variants

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

#45 - Missing some characters of amino acid name when use `panno`

Issue - State: open - Opened by wei-linlin almost 4 years ago

#44 - problem with transcript to genomic coordinates conversion when UTR spans more than 1 exon

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

#43 - Bug in annotation download code?

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

#42 - Can't index from GTF files for C. elegans

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

#41 - chr8:g.145737904C>T protein change failed

Issue - State: open - Opened by Gerosyclouds almost 5 years ago

#40 - Performance improvements (suggestion)

Issue - State: open - Opened by gzalo almost 5 years ago - 1 comment

#39 - config.py links for raw transcript tables

Issue - State: open - Opened by zmiimz almost 5 years ago

#38 - convert variant annotations from TransVar into a basic MAF

Issue - State: open - Opened by zmiimz almost 5 years ago

#37 - record.py format_group grouping settings

Issue - State: closed - Opened by zmiimz about 5 years ago - 1 comment

#36 - inconsistent InFrameInsertion annotation

Issue - State: open - Opened by shannonnana about 5 years ago - 1 comment

#35 - missing and inconsistent protein annotation usage

Issue - State: open - Opened by git-jemiller about 5 years ago - 1 comment

#34 - Inconsistent position

Issue - State: open - Opened by bitsyamagu over 5 years ago - 12 comments

#33 - Enable handling of complexed indels

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

#32 - Speed up fetch_sequence

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

#31 - Performance issue in faidx.py fetch_sequence

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

#30 - three different results for the same canno input - which one is correct?

Issue - State: open - Opened by orthoceros over 5 years ago

#29 - some error message in the info field are not self-explanatory

Issue - State: open - Opened by DavidTamborero over 5 years ago - 2 comments

#28 - How to get transcript version number?

Issue - State: open - Opened by lvran1234 over 5 years ago - 1 comment

#27 - Different position converter result?

Issue - State: closed - Opened by xiucz almost 6 years ago - 3 comments

#26 - failed annotation complex variant

Issue - State: closed - Opened by kjass001 almost 6 years ago - 3 comments

#25 - Choose Ensembl release when downloading annotations + Python 3 compatibility issues

Pull Request - State: closed - Opened by jordeu about 6 years ago - 2 comments

#24 - Problems with UniProt support

Issue - State: closed - Opened by grayfall about 6 years ago - 4 comments

#23 - hotfixing UnicodeDecodeError in annodb

Pull Request - State: closed - Opened by grayfall about 6 years ago

#22 - UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 0: invalid start byte

Issue - State: closed - Opened by grayfall about 6 years ago - 1 comment

#21 - c.-22A>G works, c.-19-3A>G doesn't

Issue - State: open - Opened by mjafin over 6 years ago - 1 comment

#20 - UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 0: invalid start byte

Issue - State: open - Opened by kantale over 6 years ago - 1 comment

#19 - inconsistence

Issue - State: open - Opened by hh1985 about 7 years ago - 2 comments

#18 - c. annotations don't align with 3' genomic annotations on reverse strand

Issue - State: open - Opened by RDuren about 7 years ago

#17 - how to annotate using rsID?

Issue - State: open - Opened by gpcr over 7 years ago

#16 - can't download reference genome/annotation

Issue - State: open - Opened by shoy91 over 7 years ago - 7 comments

#15 - Fix TypeError in deletion.py

Pull Request - State: closed - Opened by annadcunningham over 7 years ago - 1 comment

#14 - Reference sequence doesn't exist error after following example

Issue - State: closed - Opened by kuanlinhuang almost 8 years ago - 4 comments

#13 - need more annotated intomation from vcf input

Issue - State: closed - Opened by die4live almost 8 years ago - 2 comments

#12 - ganno batch example

Issue - State: closed - Opened by cboustred almost 8 years ago - 1 comment

#11 - Add Python 3 compatibility. Mostly by runing 2to3 and replacing '/' w…

Pull Request - State: closed - Opened by ostrokach almost 8 years ago - 1 comment

#10 - `transvar/docs/source/features.rst` content incomplete

Issue - State: closed - Opened by die4live about 8 years ago - 3 comments

#9 - Querying upstream and downstream (including 5'UTR and 3'UTR)

Issue - State: open - Opened by chelseaju about 8 years ago - 1 comment

#8 - what's the difference between gDNA and left_align_gDNA

Issue - State: closed - Opened by die4live about 8 years ago - 1 comment

#7 - RefSeq hg19

Issue - State: closed - Opened by sarmadym over 8 years ago - 1 comment

#6 - Programatic access / Python API

Issue - State: open - Opened by jpiper over 8 years ago - 1 comment

#5 - build-in dbsnp download fail

Issue - State: open - Opened by die4live over 8 years ago - 2 comments

#4 - No `CdsStartLoss` and `CdsStopLoss` functionality

Issue - State: closed - Opened by jpiper over 8 years ago - 1 comment

#3 - Fix `--mem`

Pull Request - State: open - Opened by jpiper over 8 years ago

#2 - use custom config path and use memory map files to speed up genomereference retrival

Pull Request - State: closed - Opened by jordeu over 8 years ago - 1 comment

#1 - my test issue track

Issue - State: closed - Opened by zwdzwd over 8 years ago - 1 comment

GitHub / zwdzwd/transvar issues and pull requests