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
#339 - Collapse step didn't output a gtf file without a reference annotation
Issue -
State: open - Opened by dudududu12138 about 1 month ago
#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
#334 - Hello, after splitting the BED file by chromosomes, we found that a single chromosome's BED file is 1.03G, which is larger than 1G. Can Flair Collapse currently handle a BED file of 1.03G?
Issue -
State: open - Opened by 991031liurui 2 months ago
- 1 comment
#333 - The naming of my isoforms is different from what is mentioned in your manual.
Issue -
State: open - Opened by gnilihzeux 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
#290 - flair correct crash with AttributeError: 'bool' object has no attribute 'find_overlap'
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
#288 - The results of my test_output are not consisitent with the oferred test_expected. Why?
Issue -
State: closed - Opened by qingwangchen 10 months ago
- 1 comment
#287 - Refactor
Pull Request -
State: closed - Opened by Jeltje 10 months ago
#286 - Refactor
Pull Request -
State: closed - Opened by Jeltje 10 months ago
#285 - diff_iso_usage documentation does not clear describe what it does
Issue -
State: open - Opened by diekhans 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
#283 - diff_iso_usage does not include header in output files
Issue -
State: open - Opened by diekhans 10 months ago
#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
#280 - flair collapse creates invalid isoforms names that cause GTF conversion to fail
Issue -
State: closed - Opened by diekhans 11 months ago
Labels: bug
#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
#275 - FLAIR silently continues if no short read junctions are added
Issue -
State: open - Opened by diekhans 11 months ago
#274 - flair correct claims success even when there is an error
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
#270 - flair correct documention doesn't define what <prefix>_ is
Issue -
State: open - Opened by diekhans 11 months ago
#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
#265 - Questions about flair collapse in regards of TSS/TES calling algorithm
Issue -
State: open - Opened by seungbeom-han 12 months ago
- 3 comments
#264 - Identification of full-length intergenic isoform
Issue -
State: closed - Opened by Dongxu-Zheng 12 months ago
- 1 comment
#263 - TypeError: get_sequence_with_variants() takes 2 positional arguments but 3 were given
Issue -
State: closed - Opened by youyupei 12 months ago
- 2 comments
#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
#255 - Issues when running diff_iso_usage, needs to run identify_annotated_gene.py first?
Issue -
State: closed - Opened by CWYuan08 over 1 year ago
- 1 comment
#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
#248 - predictproductivity python script error after flair collapse step
Issue -
State: closed - Opened by BijalThakkar over 1 year ago
#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
#237 - Threading issues with ssCorrect.py: RuntimeError: cannot join thread before it is started
Issue -
State: closed - Opened by chrisamiller over 1 year ago
- 4 comments