Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nedialkova-lab/mim-tRNAseq issues and pull requests

#74 - problem with Final deconvolution and filtering

Issue - State: open - Opened by zhouuplus about 1 month ago - 2 comments

#73 - Interpretation of the "proportion" Column in mismatchTable.csv

Issue - State: closed - Opened by Xinkai-Wu 2 months ago - 2 comments

#72 - how does mim-tRNAseq handle partially mapped tRNA sequence?

Issue - State: open - Opened by lkong888 3 months ago - 1 comment

#71 - Fail to read the header from unpaired_mult files

Issue - State: open - Opened by Xinkai-Wu 3 months ago - 1 comment

#70 - Formatting of tRNA FASTA reference file

Issue - State: closed - Opened by Phontia 4 months ago - 9 comments

#68 - Installation of mimseq package

Issue - State: closed - Opened by Phontia 4 months ago - 3 comments

#67 - GMAP version 2017-11-15

Issue - State: closed - Opened by Futa0908 12 months ago - 4 comments

#66 - GSNAP Ver. 2019-02-26 Installation issues

Issue - State: closed - Opened by Futa0908 about 1 year ago - 2 comments

#65 - Interpretation of output files

Issue - State: open - Opened by pawanchk about 1 year ago - 2 comments

#64 - modifications outdated?

Issue - State: closed - Opened by piechottam about 1 year ago - 2 comments

#63 - fix: open local modifications file in read-only

Pull Request - State: closed - Opened by kelly-sovacool about 1 year ago

#62 - Error in differential expression analysis

Issue - State: closed - Opened by kelly-sovacool about 1 year ago - 2 comments

#61 - cmalign dependency when installing from source

Issue - State: closed - Opened by kelly-sovacool about 1 year ago - 4 comments

#60 - ci: create simple E2E test for github actions

Pull Request - State: open - Opened by kelly-sovacool about 1 year ago - 2 comments

#60 - ci: create simple E2E test for github actions

Pull Request - State: closed - Opened by kelly-sovacool about 1 year ago - 23 comments

#59 - Incomplete refactor in tRNAtools

Issue - State: closed - Opened by kelly-sovacool about 1 year ago - 1 comment

#59 - Incomplete refactor in tRNAtools

Issue - State: closed - Opened by kelly-sovacool about 1 year ago - 1 comment

#58 - Set up E2E test with continuous integration

Issue - State: closed - Opened by kelly-sovacool about 1 year ago - 3 comments

#57 - fix: remove unused modomics variable

Pull Request - State: closed - Opened by kelly-sovacool about 1 year ago - 1 comment

#56 - bug: out_dir is a boolean in modsToSNPIndex()

Issue - State: closed - Opened by kelly-sovacool about 1 year ago

#55 - fix: require requests

Pull Request - State: closed - Opened by kelly-sovacool about 1 year ago - 1 comment

#54 - fix: remove & ignore build artifacts

Pull Request - State: closed - Opened by kelly-sovacool about 1 year ago - 1 comment

#53 - Merge pull request #52 from nedialkova-lab/revert-51-revert-50-read-m…

Pull Request - State: closed - Opened by drewjbeh about 1 year ago

#52 - Revert "Revert "fix: open modomics file in read-only mode""

Pull Request - State: closed - Opened by drewjbeh about 1 year ago

#51 - Revert "fix: open modomics file in read-only mode"

Pull Request - State: closed - Opened by drewjbeh about 1 year ago

#50 - fix: open modomics file in read-only mode

Pull Request - State: closed - Opened by kelly-sovacool about 1 year ago - 2 comments

#49 - Installation errors

Issue - State: closed - Opened by pawanchk about 1 year ago - 18 comments

#48 - Problems about match to Modomics dataset

Issue - State: closed - Opened by Yanhui-1008 about 1 year ago - 12 comments

#48 - Problems about match to Modomics dataset

Issue - State: open - Opened by Yanhui-1008 about 1 year ago - 11 comments

#47 - Error in the Alignment step

Issue - State: closed - Opened by marctormo about 1 year ago - 2 comments

#46 - Issue after update

Issue - State: closed - Opened by joegeorgeson about 1 year ago - 11 comments

#45 - Error occur when"Parsing Modomics JSON data"

Issue - State: closed - Opened by wuxujia-dev about 1 year ago - 15 comments

#43 - A potential problem when working on self-made tRNA fasta

Issue - State: closed - Opened by ruixuan-zhang over 1 year ago - 4 comments

#42 - multiprocessing.pool.RemoteTraceback error

Issue - State: closed - Opened by huLi2023 over 1 year ago - 5 comments

#40 - Dockerized mim-tRNAseq

Issue - State: closed - Opened by joegeorgeson over 1 year ago - 10 comments

#39 - Add documentation of SLAC algorithm

Pull Request - State: closed - Opened by hexavier almost 2 years ago - 1 comment

#38 - Incorporate crosstalks analysis into mim-tRNAseq

Pull Request - State: closed - Opened by hexavier almost 2 years ago - 2 comments

#37 - subprocess.CalledProcessError

Issue - State: closed - Opened by Squirrelity about 2 years ago - 7 comments

#36 - Ts split mt plastid

Pull Request - State: closed - Opened by TomSmithCGAT about 2 years ago - 1 comment

#35 - Isodecoder column in counts incorrect

Issue - State: closed - Opened by TomSmithCGAT over 2 years ago - 3 comments
Labels: bug

#34 - KeyError

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

#33 - Error

Issue - State: closed - Opened by kopardev over 2 years ago - 7 comments

#32 - Docker?

Issue - State: closed - Opened by kopardev over 2 years ago - 2 comments
Labels: enhancement

#31 - usearch vs vsearch

Issue - State: closed - Opened by TomSmithCGAT over 2 years ago - 11 comments
Labels: enhancement

#30 - non-zero exist status 9 error

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

#29 - Run it for other species

Issue - State: closed - Opened by AnneHoffmann over 2 years ago - 3 comments

#28 - Questions about Spikein

Issue - State: closed - Opened by AngLiRNA almost 3 years ago - 1 comment

#27 - CalledProcessError: Command '['gsnap'.....] returned non-zero exit status 9.

Issue - State: closed - Opened by AngLiRNA almost 3 years ago - 2 comments

#26 - Conda Installation - R version problem

Issue - State: closed - Opened by cyken6621 almost 3 years ago - 2 comments

#25 - memory problems fixed by sorting before coverage check

Pull Request - State: closed - Opened by jabard89 almost 3 years ago - 1 comment

#24 - question in CCAanalysis output

Issue - State: closed - Opened by oneleaf425 almost 3 years ago - 2 comments
Labels: question

#23 - AttributeError: 'DataFrame' object has no attribute 'name'

Issue - State: closed - Opened by Pablolo99 about 3 years ago - 2 comments

#22 - Read mapping vs. alignment

Issue - State: closed - Opened by krdav about 3 years ago - 4 comments

#21 - Error with tRNAscan-SE format results

Issue - State: closed - Opened by Pablolo99 about 3 years ago - 1 comment

#20 - Ask a fundamental question about the code

Issue - State: closed - Opened by songrunxian about 3 years ago

#19 - Problems with gmap_build

Issue - State: closed - Opened by MKoesters over 3 years ago - 1 comment

#18 - Update README.md

Pull Request - State: closed - Opened by MKoesters over 3 years ago - 1 comment

#17 - nothing provides pyfiglet needed by mimseq-0.2.5.3-pyr40_0

Issue - State: closed - Opened by MKoesters over 3 years ago - 2 comments

#16 - IndexError: Too many levels: Index has only 1 level, not 2

Issue - State: closed - Opened by Ashring-Tang over 3 years ago - 5 comments

#15 - splitClusters.py 'KeyError sequence' error while running sample data

Issue - State: closed - Opened by cyken6621 over 3 years ago - 12 comments
Labels: bug

#14 - Threshold of the Fig4A and B

Issue - State: closed - Opened by YueZhang2019 over 3 years ago - 3 comments
Labels: enhancement

#13 - OSError: [Errno 8] Exec format error: 'usearch'

Issue - State: closed - Opened by Ashring-Tang over 3 years ago - 1 comment

#12 - mimseq testing error: No such file or directory: 'cmalign'

Issue - State: closed - Opened by yc-2000 over 3 years ago - 1 comment

#11 - some inssues about usearch

Issue - State: closed - Opened by Ashring-Tang over 3 years ago - 1 comment

#10 - A basic issue about analysis SAMPLE DATA by mimseq

Issue - State: closed - Opened by Ashring-Tang over 3 years ago - 2 comments

#9 - KeyError in unknownMods(), mmquant.py

Issue - State: closed - Opened by uschwartz over 3 years ago - 5 comments

#8 - figure of anticodon_vst_hp.png

Issue - State: closed - Opened by YueZhang2019 over 3 years ago - 5 comments

#8 - figure of anticodon_vst_hp.png

Issue - State: closed - Opened by YueZhang2019 over 3 years ago - 5 comments

#7 - mmQuant.py error

Issue - State: closed - Opened by onuryukselen over 3 years ago - 10 comments

#6 - mimseq error: Faceting variables must have at least one value

Issue - State: closed - Opened by mt1022 over 3 years ago - 8 comments

#6 - mimseq error: Faceting variables must have at least one value

Issue - State: closed - Opened by mt1022 over 3 years ago - 8 comments

#5 - Installation error: Bio.Alphabet has been removed from Biopython

Issue - State: closed - Opened by mt1022 over 3 years ago - 1 comment
Labels: bug

#4 - Command '['gsnap', '...']' returned non-zero exit status 255.

Issue - State: closed - Opened by sarahbonnin almost 4 years ago - 9 comments
Labels: enhancement

#3 - Unsupported format character

Issue - State: closed - Opened by dpryan79 almost 4 years ago - 2 comments

#2 - pycache update

Pull Request - State: closed - Opened by drewjbeh almost 5 years ago