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
#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
- 3 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 almost 2 years ago
#238 - Escaping asterisks in file names
Issue -
State: closed - Opened by chrisamiller almost 2 years ago
- 4 comments
#237 - Threading issues with ssCorrect.py: RuntimeError: cannot join thread before it is started
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
#228 - Should I turn on or turn off the "--u_substitution" for guppy basecalling if I use Flair for my downstream analysis?
Issue -
State: closed - Opened by yjx1217 almost 2 years ago
- 1 comment
#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
#223 - inconsistency of isoform_ids formatting of flair diffSplice regarding "es" relative to "alt3", "alt5", and "ir"
Issue -
State: closed - Opened by yjx1217 almost 2 years ago
- 1 comment
#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
#173 - predictProductivity.py Error: cannot construct subsequence with negative offset or length < 1
Issue -
State: closed - Opened by zoucheng123 about 3 years ago
- 2 comments
#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.