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

#260 - Feature request: define group for diffExp contrast

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

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

Issue - State: closed - Opened by pothepanda09 over 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 over 1 year ago - 3 comments
Labels: Old ticket; not enough info to proceed.

#257 - Collapse creating combined isoforms

Issue - State: closed - Opened by eschiks over 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 - 3 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 almost 2 years ago

#238 - Escaping asterisks in file names

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

#236 - Question about filter option in collapsing step

Issue - State: open - Opened by eprdz almost 2 years ago

#235 - diffSplice showing the same value for all replicates

Issue - State: closed - Opened by fburdet almost 2 years ago - 1 comment

#234 - DRIMSeq output has same value for all replicates

Issue - State: open - Opened by mnsmar almost 2 years ago - 1 comment
Labels: enhancement

#233 - open(os.path.join(tempDir, "%s_inconsistent.bed" % chrom),'rb') as fd

Issue - State: closed - Opened by gaobaoqing-picb almost 2 years ago - 7 comments

#232 - gtf_to_bed and bed_to_sequence commands not in the conda environment

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

#231 - Feature request: add genes to flair diffSplice output

Issue - State: open - Opened by Jeltje almost 2 years ago
Labels: enhancement

#230 - Flair collapse requires >1TB of RAM

Issue - State: open - Opened by oneillkza almost 2 years ago - 6 comments

#229 - add TES junction support

Pull Request - State: closed - Opened by seungbeom-han almost 2 years ago

#227 - --fusion_dist option in collapse module

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

#226 - Collapse with range option does not give isoform.fa and isoform.gtf

Issue - State: closed - Opened by hd00ljy almost 2 years ago - 4 comments

#225 - collapse range for multiple samples

Issue - State: closed - Opened by hd00ljy almost 2 years ago

#224 - Slow processing speed for the large number of samples (collapse stage)

Issue - State: closed - Opened by hd00ljy almost 2 years ago - 2 comments

#222 - Flair collapse --annotation_reliant doesn't run without --generate_map

Issue - State: closed - Opened by cafelton about 2 years ago - 1 comment

#221 - Error running flair collapse with both --annotation_reliant and --check_splice

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

#220 - DRIMSeq was triggered even without specifiying '--test' for flair diffSplice

Issue - State: closed - Opened by yjx1217 about 2 years ago - 3 comments

#219 - Unable to run bam2bed12

Issue - State: closed - Opened by gcorre about 2 years ago - 3 comments
Labels: bug

#218 - diffSplice 'returned non-zero exit status'

Issue - State: closed - Opened by MustafaElshani about 2 years ago - 9 comments

#217 - FLAIR correct error with chr1_inconsistent.bed?

Issue - State: closed - Opened by seongwoohan about 2 years ago - 1 comment

#216 - RGB code issue in .bed12 output for single exons

Issue - State: open - Opened by suegrimes about 2 years ago
Labels: bug

#215 - Flair Collapse: NameError: name 'res' is not defined

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

#214 - diffExp incomplete output

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

#213 - predictProductivity 'inconsistent naming convention' error

Issue - State: closed - Opened by MustafaElshani about 2 years ago - 11 comments

#212 - deFLAIR cannot run on more than two groups

Issue - State: open - Opened by Jeltje about 2 years ago
Labels: bug

#211 - assign reads into isoforms without mapping

Issue - State: closed - Opened by xieyy46 about 2 years ago - 2 comments
Labels: Old ticket; not enough info to proceed.

#210 - Truncated, non-full length reads

Issue - State: closed - Opened by vicasze about 2 years ago - 6 comments

#209 - Interpreting output

Issue - State: closed - Opened by ajritter8 about 2 years ago - 9 comments

#207 - flair correct error

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

#202 - Fatal error: unable to initialize the JIT

Issue - State: closed - Opened by wenmm over 2 years ago - 1 comment
Labels: Old ticket; not enough info to proceed.

#201 - list index out of range while retraining TARSClassifier

Issue - State: closed - Opened by zeos over 2 years ago - 1 comment

#200 - ssCorrect.py FileNotFoundError when running flair correct

Issue - State: closed - Opened by peterthorpe5 over 2 years ago - 5 comments
Labels: Old ticket; not enough info to proceed.

#197 - error in diff_Splice

Issue - State: closed - Opened by changeran over 2 years ago - 1 comment
Labels: Old ticket; not enough info to proceed.

#195 - diffsplice_fishers_exact.py produces adjusted pvalue?

Issue - State: closed - Opened by MarLee39 over 2 years ago - 1 comment

#191 - 5' ends not well defined

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

#188 - flair collapse stops without error message

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

#186 - Error in ssCorrect.py when using Docker

Issue - State: closed - Opened by Eduardo-vsouza over 2 years ago - 1 comment

#180 - Error in correct, line 377 Too many open files

Issue - State: closed - Opened by J-Calvelo almost 3 years ago - 1 comment
Labels: bug

#179 - Another error when using collapse

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

#178 - error when using flair collapse

Issue - State: closed - Opened by wuhao08 almost 3 years ago - 10 comments

#177 - diffsplice not producing the p-value with --test

Issue - State: closed - Opened by dar19 about 3 years ago - 1 comment
Labels: Old ticket; not enough info to proceed.

#176 - .yaml file does not solve

Issue - State: closed - Opened by pgupta3005 about 3 years ago - 3 comments

#174 - Flair.py collapse error - NameError: name 'res' is not defined

Issue - State: closed - Opened by andy941 about 3 years ago - 4 comments
Labels: bug

#171 - DiffExp - problems with rpy2 and R

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

#170 - collapse fails silently if fastq is missing or not an absolute path

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

#169 - python version confusion

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

#167 - Get read IDs along with transcript IDs

Issue - State: closed - Opened by Akanksha2511 over 3 years ago - 1 comment

#165 - Flair collapse and quantify "--stringent" option.

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

#163 - flair quantify --tpm option

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

#162 - too many single-exon transcripts

Issue - State: closed - Opened by robinycfang over 3 years ago - 6 comments

#161 - No differential isoform usage output?

Issue - State: closed - Opened by wigge206 over 3 years ago - 2 comments

#156 - losing crucial reads due to correct step

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

#155 - predictProductivity.py error

Issue - State: closed - Opened by zoucheng123 over 3 years ago - 5 comments

#154 - diffSplice

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

#153 - diffExp

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

#152 - NameError: name 'tqdm' is not defined in ssCorrect.py

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

#151 - Rpy2 vs numpy: compatibility issues

Issue - State: closed - Opened by leticia-castro over 3 years ago - 3 comments

#146 - Combined samples and then map or map samples separately?

Issue - State: closed - Opened by callumparr almost 4 years ago - 1 comment

#145 - File or directory missing during initial step

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

#138 - Error on Collapse command

Issue - State: closed - Opened by RichardCorbett almost 4 years ago - 1 comment

#136 - short read correction

Issue - State: closed - Opened by charreca almost 4 years ago - 3 comments
Labels: wontfix

#131 - Error in diffExp

Issue - State: closed - Opened by shamsbhuiyan about 4 years ago - 1 comment
Labels: Old ticket; not enough info to proceed.

#130 - Annotate 5'UTR, CDS, 3UTR in FLAIR isoform

Issue - State: open - Opened by akk01 about 4 years ago - 5 comments
Labels: enhancement

#121 - Questions about "samJuncs.py"

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

#106 - flair collapse output doesn't contain any info from the gtf

Issue - State: closed - Opened by wolfgangrumpf over 4 years ago - 7 comments
Labels: Old ticket; not enough info to proceed.

#104 - novel transcripts located in UTR and reads mapped to wrong places

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

#101 - diff_iso_usage.py produces unexpected results with 0.0 counts

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

#100 - diffExp-rpy2.rinterface.RRuntimeError

Issue - State: closed - Opened by ozgegizlenci over 4 years ago - 9 comments

#96 - Differences between the diffsplice outputs

Issue - State: closed - Opened by shamsbhuiyan over 4 years ago - 9 comments

#95 - diffsplice_fishers_exact.py error

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

#94 - Flair quantify missing counts for one isoform

Issue - State: closed - Opened by wigge206 over 4 years ago - 3 comments

#88 - Transcript IDs not assigned properly by Flair Collapse

Issue - State: closed - Opened by ADelgadoT almost 5 years ago - 3 comments

#80 - Promoter BED for mice

Issue - State: closed - Opened by peterkilfeather almost 5 years ago - 1 comment

#79 - predictProductivity.py error

Issue - State: closed - Opened by ozgegizlenci almost 5 years ago - 9 comments

#77 - flair-quantify misses some isoforms from flair-collapse

Issue - State: closed - Opened by yejilee-biostat almost 5 years ago - 3 comments

#64 - Flair collapse - annotated ends from GTF stall

Issue - State: closed - Opened by number-25 almost 5 years ago - 2 comments
Labels: Old ticket; not enough info to proceed.