Ecosyste.ms: Issues

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

GitHub / BrooksLabUCSC/flair issues and pull requests

#340 - FLAIR missing isoforms

Issue - State: open - Opened by lilif99 about 1 month ago - 1 comment

#338 - ValueError in filter_isoforms_by_proportion_of_gene_expr.py

Issue - State: open - Opened by byee4 about 1 month ago

#337 - flair quantify problem error

Issue - State: open - Opened by wdesaintjean about 1 month ago

#336 - flair correct shows FileNotFoundError

Issue - State: open - Opened by guo0814 about 2 months ago

#335 - psl_to_sequence command

Issue - State: open - Opened by sparthib about 2 months ago

#332 - How to concatenate bed files before flair collapse

Issue - State: open - Opened by chenxing-zhang 2 months ago - 2 comments

#331 - allow flair correct to specify temporary directory

Issue - State: open - Opened by diekhans 2 months ago - 1 comment

#330 - Incorrectly name flair align options is confusing

Issue - State: open - Opened by diekhans 2 months ago

#329 - How to count the isoforms corresponding to each gene.

Issue - State: closed - Opened by anxuan-web 4 months ago - 2 comments

#328 - flair collapse--NameError: name 'blockcount' is not defined

Issue - State: closed - Opened by ChenOreo 4 months ago - 4 comments

#327 - Flair collapse issue

Issue - State: closed - Opened by TTT16 5 months ago - 13 comments

#326 - add --split-prefix to collapse minimap command

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

#325 - fix #180, thanks Colette

Pull Request - State: closed - Opened by Jeltje 5 months ago

#324 - error in flair quantify

Issue - State: closed - Opened by jakobht96 5 months ago - 9 comments

#323 - Gene model naming issue

Issue - State: open - Opened by sagnikbanerjee15 5 months ago - 1 comment

#322 - Crash running flair collapse

Issue - State: open - Opened by mbkodos 5 months ago - 8 comments

#321 - Set isoform abundance cutoff to FLAIR quantify

Issue - State: open - Opened by ulbivin 5 months ago - 1 comment

#320 - A question about correct model

Issue - State: open - Opened by anxuan-web 5 months ago - 4 comments

#319 - fixed #318; updated faq

Pull Request - State: closed - Opened by Jeltje 6 months ago

#318 - Flair quantify error message bug

Issue - State: closed - Opened by Chemical118 6 months ago - 1 comment

#316 - ITD detection?

Issue - State: open - Opened by itslittman 7 months ago - 12 comments

#315 - Not full length transcript

Issue - State: closed - Opened by yycc9897 7 months ago - 2 comments

#314 - Running collapse_isoforms_precise.py in a main entry point

Issue - State: closed - Opened by andyjslee 7 months ago - 2 comments

#313 - merging code of conduct and discussion

Pull Request - State: closed - Opened by Jeltje 7 months ago

#311 - Flair collapse stuck at "renaming isoforms using gtf" without error

Issue - State: closed - Opened by dmanahan1 7 months ago - 3 comments

#309 - diffSplice : No such file or directory: 'call_diffsplice_events.py'

Issue - State: closed - Opened by CorentinAube 8 months ago - 1 comment

#308 - Running Flair with multiple samples and replicates

Issue - State: closed - Opened by benpiticaru 8 months ago - 1 comment

#307 - diffSplice files are empty

Issue - State: closed - Opened by ghofrankothoum 8 months ago - 1 comment

#306 - FLAIR could improve alignments by passing minimap2 splice junctions

Issue - State: open - Opened by diekhans 9 months ago - 3 comments
Labels: enhancement

#305 - Unexpected entries in gtf file after flair collapse

Issue - State: closed - Opened by juanfraitu1 9 months ago - 1 comment

#304 - Issues implementing FLAIR2

Issue - State: closed - Opened by Max-Tomlinson 9 months ago - 1 comment
Labels: Old ticket; not enough info to proceed.

#303 - Question regarding sequencing depth and collapse step

Issue - State: closed - Opened by wuy24 9 months ago - 1 comment

#302 - Transcript read number

Issue - State: closed - Opened by seongwoohan 9 months ago

#301 - equal with base

Pull Request - State: closed - Opened by Jeltje 9 months ago

#300 - Refactor

Pull Request - State: closed - Opened by Jeltje 9 months ago

#299 - Translate predictProductivity output to protein

Issue - State: closed - Opened by andreas-wilm 10 months ago - 4 comments

#298 - Make FLAIR source & packaging structure not weird

Issue - State: open - Opened by diekhans 10 months ago
Labels: enhancement

#297 - readthedocs change

Pull Request - State: closed - Opened by Jeltje 10 months ago

#296 - MarkD updates for py3.11 and some code cleanup

Pull Request - State: closed - Opened by Jeltje 10 months ago

#295 - work around for python 3.11 and a few other things

Pull Request - State: closed - Opened by diekhans 10 months ago

#294 - Improve documentation of algorithm is readthedocs

Issue - State: open - Opened by diekhans 10 months ago
Labels: AddToManual

#293 - flair correct doesn't exit non-zero when an invalid argument is supplied

Issue - State: open - Opened by diekhans 10 months ago - 3 comments

#292 - Refactor branch with fixes for #290 and #291

Pull Request - State: closed - Opened by Jeltje 10 months ago

#291 - ssUtils.py gtfToSSBed crashes if gtf doesn't have transcript_id

Issue - State: closed - Opened by diekhans 10 months ago - 1 comment

#289 - Refactor - improved error messaging

Pull Request - State: closed - Opened by Jeltje 10 months ago

#287 - Refactor

Pull Request - State: closed - Opened by Jeltje 10 months ago

#286 - Refactor

Pull Request - State: closed - Opened by Jeltje 10 months ago

#284 - merging of transcript ids and gene ids is frustrating to use

Issue - State: closed - Opened by diekhans 10 months ago - 2 comments

#282 - diffsplice_fishers_exact generates bogus error if input file is missing

Issue - State: open - Opened by diekhans 11 months ago - 1 comment

#281 - `'run_id' is not defined` error while running `collapse-range`

Issue - State: closed - Opened by lvclark 11 months ago - 2 comments

#279 - can't keep intermediate files when calling correct from flair

Issue - State: open - Opened by diekhans 11 months ago - 1 comment
Labels: enhancement

#278 - accept BED9 as well as BED6 for splice junctions

Issue - State: open - Opened by diekhans 11 months ago
Labels: enhancement

#277 - FLAIR need obvious succes or failure message

Issue - State: closed - Opened by diekhans 11 months ago - 2 comments

#276 - FLAIR logging is very hard to use

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

#273 - Please do not guess file types

Issue - State: open - Opened by diekhans 11 months ago - 1 comment

#272 - junctions_from_sam creates invalid BEDs that are silently ignored

Issue - State: closed - Opened by diekhans 11 months ago - 5 comments
Labels: bug

#271 - flair 123 appears not to use splice junctions

Issue - State: closed - Opened by diekhans 11 months ago - 1 comment

#269 - flair 123 is horribly hard to use

Issue - State: open - Opened by diekhans 11 months ago - 1 comment

#268 - alarming "errors" when running multiple modules

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

#267 - Error while running collapse

Issue - State: closed - Opened by kundariyahardik 11 months ago - 3 comments

#266 - diffsplice output format not documented

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

#264 - Identification of full-length intergenic isoform

Issue - State: closed - Opened by Dongxu-Zheng 12 months ago - 1 comment

#262 - Flair collapse returns isoform as same as reference

Issue - State: closed - Opened by NHoang98 12 months ago - 2 comments

#261 - Error in filter_isoforms_by_proportion_of_gene_expr.py

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

#260 - Feature request: define group for diffExp contrast

Issue - State: closed - Opened by skchronicles about 1 year ago - 5 comments

#259 - /Error at the FLAIR collapse step (no data in output files)

Issue - State: closed - Opened by pothepanda09 about 1 year ago - 2 comments
Labels: Old ticket; not enough info to proceed.

#258 - Fresh flair install fails align test. [makefile:26: test-align] Error 1

Issue - State: closed - Opened by Hans4984 about 1 year ago - 3 comments
Labels: Old ticket; not enough info to proceed.

#257 - Collapse creating combined isoforms

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

#256 - Question regarding number of reads.

Issue - State: open - Opened by eprdz over 1 year ago

#254 - Splicing events belong to more than 1 gene

Issue - State: open - Opened by orbitalse over 1 year ago

#253 - diffSplice: start coordinates > end coordinates

Issue - State: open - Opened by orbitalse over 1 year ago

#252 - FileNotFoundError: [Errno 2] No such file or directory: 'linker'

Issue - State: closed - Opened by saizalbert over 1 year ago - 1 comment

#251 - Update count_sam_transcripts.py

Pull Request - State: closed - Opened by listen2099 over 1 year ago - 1 comment

#250 - diffsplice_fishers_exact error when dealing with ir.events.quant.tsv

Issue - State: open - Opened by QingCheZhang over 1 year ago - 2 comments

#249 - Unable to install Flair using bioconda

Issue - State: closed - Opened by jwyli over 1 year ago - 1 comment

#247 - Revert "Stranded alignment for dRNA in flair quantify"

Pull Request - State: closed - Opened by MViscardi-UCSC over 1 year ago

#246 - Stranded alignment for dRNA in flair quantify

Pull Request - State: closed - Opened by MViscardi-UCSC over 1 year ago - 1 comment

#245 - Unable to find minimap2 in conda environment

Issue - State: closed - Opened by RDorney over 1 year ago

#244 - "Superset isoform" definition in flair filter_collapsed_isoforms.py

Issue - State: open - Opened by mariachiaragrieco over 1 year ago - 2 comments

#243 - Testing Flair: missing file

Issue - State: closed - Opened by RDorney over 1 year ago - 2 comments

#242 - Flair align fails with pysam libcrypto.so.1.0.0 not found

Issue - State: closed - Opened by vpeddu over 1 year ago - 2 comments

#240 - predictProductivity seems incompatible with rvolden/Mandalorion-derived GTF

Issue - State: closed - Opened by ajritter8 over 1 year ago - 6 comments

#239 - adds quoting to handle wildcard characters in filenames

Pull Request - State: closed - Opened by chrisamiller over 1 year ago

#238 - Escaping asterisks in file names

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