Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / Bioconductor/GenomicFeatures issues and pull requests
#68 - How to import pseudogenes from GFF3 file as GRanges object?
Issue -
State: open - Opened by zhewa 3 months ago
#67 - GenomicFeatures:::load_package_gracefully apparently fails on BBS
Issue -
State: closed - Opened by FelixErnst 4 months ago
- 2 comments
#66 - Feature Request: Implementation of getTerminatorSeq() Function
Issue -
State: closed - Opened by JavierMenRev 6 months ago
- 6 comments
#65 - How to make a TxDb object for the T2T-CHM13v2.0 genome (telomere to telomere Human genome)
Issue -
State: closed - Opened by hpages 7 months ago
#64 - Installation requires vctrs (≥ 0.6.0)
Issue -
State: closed - Opened by amitfrishberg 9 months ago
- 4 comments
#63 - GenomicFeature error with mm10
Issue -
State: closed - Opened by MurliNair 11 months ago
- 7 comments
#62 - makeTxDbFromUCSC failed for susScr11
Issue -
State: closed - Opened by sinnis007 11 months ago
- 3 comments
#61 - makeTxDbFromUCSC failed for mm9
Issue -
State: closed - Opened by Moonriver1988 12 months ago
- 4 comments
#60 - Extracting exons result is different from manual extraction
Issue -
State: closed - Opened by gernophil about 1 year ago
- 5 comments
#59 - fiveUTRsByTranscript() and threeUTRsByTranscript() give incorrect UTRs
Issue -
State: closed - Opened by a92932000 about 1 year ago
- 3 comments
#58 - installation issue
Issue -
State: closed - Opened by LliliansCalvo about 1 year ago
- 1 comment
#57 - `makeTxDbFromBiomart()` on the Ensembl archive version failed
Issue -
State: closed - Opened by timedreamer about 1 year ago
- 14 comments
#56 - `makeTxDbFromGFF` fails with (bacterial) genome GTF files from NCBI
Issue -
State: closed - Opened by m-jahn over 1 year ago
- 5 comments
#55 - Add 'genome' argument to makeTxDbFromGFF()
Issue -
State: closed - Opened by hpages over 1 year ago
- 3 comments
#54 - mapToTranscripts reports incorrect regions when supplied GRangesList containing some empty transcripts
Issue -
State: open - Opened by kriemo over 1 year ago
#53 - Create custom TxDb Package from NCBI GFF file
Issue -
State: closed - Opened by sopeadeniji over 1 year ago
- 2 comments
#52 - makeTxDbPackageFromUCSC failed
Issue -
State: closed - Opened by haowulab almost 2 years ago
- 3 comments
#51 - makeTxDbFromGFF fails, possibly due to download.file / restfulr?
Issue -
State: closed - Opened by AMChalkie about 2 years ago
- 3 comments
#50 - makeTxDbFromUCSC fails to connect to UCSC server
Issue -
State: closed - Opened by ameliaregina about 2 years ago
- 6 comments
#49 - makeTxDbFromEnsembl for Ensembl AnnotationHub objects?
Issue -
State: closed - Opened by mschubert about 2 years ago
- 1 comment
#48 - makeTxDbFromBiomart error when querying fungi hosts
Issue -
State: closed - Opened by LiNk-NY about 2 years ago
- 6 comments
#47 - Find coordinates of all known transcription start and termination sites (TSS TTS) for a gene
Issue -
State: closed - Opened by pgupta3005 about 2 years ago
- 4 comments
#46 - How to find the reference to an organism in the organism database?
Issue -
State: closed - Opened by prmunn about 2 years ago
- 2 comments
#45 - ExtractTranscriptSeqs extracted sequences with non-base
Issue -
State: closed - Opened by lbwfff about 2 years ago
- 1 comment
#44 - threeUTRsByTranscript() and fiveUTRsByTranscript() are not working correctly on minus strand
Issue -
State: closed - Opened by anmej about 2 years ago
- 1 comment
#43 - exonsBy Option to Resize Exons for Splicing Donor and Acceptor Regions
Issue -
State: closed - Opened by DarioS over 2 years ago
- 3 comments
#41 - error unknown
Issue -
State: closed - Opened by under-score over 2 years ago
- 3 comments
#40 - promoters() returns out of range indicies
Issue -
State: closed - Opened by cmatKhan over 2 years ago
- 3 comments
#39 - transition the package to useEnsembl
Pull Request -
State: closed - Opened by LiNk-NY over 2 years ago
#38 - makeTxDbFromUCSC failing on check of txtable
Issue -
State: closed - Opened by jmacdon over 2 years ago
- 2 comments
#37 - GENE IDs are not loaded from UCSC tables using makeTxDbPackageFromUCSC
Issue -
State: closed - Opened by farshadf over 2 years ago
- 6 comments
#36 - makeTxDbFromGFF() how to handle entries lacking or duplicated "transcript_id" attribute
Issue -
State: closed - Opened by madzafv over 2 years ago
- 2 comments
#35 - Why 'downstream' is set to 200 by default in getPromoterSeq()
Issue -
State: closed - Opened by hpages over 2 years ago
- 4 comments
#34 - `makeTxDbFromUCSC` fails with `!anyNA(m32) is not TRUE`
Issue -
State: closed - Opened by edikedik over 2 years ago
- 1 comment
#33 - protein_coding_gene not recognized as valid gene feature
Issue -
State: closed - Opened by cmatKhan almost 3 years ago
- 1 comment
#32 - Fail to add stop_codon through makeTxDbFromGRanges
Issue -
State: closed - Opened by ggoodstudydaydayup almost 3 years ago
- 5 comments
#31 - Get gene_name column from GENCODE GTF?
Issue -
State: closed - Opened by Zepeng-Mu about 3 years ago
- 1 comment
#30 - Unable to parse bacterial GFF files
Issue -
State: closed - Opened by jambler24 over 3 years ago
- 1 comment
#29 - Affected changes from the new UCSC Table Query interface of rtracklayer package
Pull Request -
State: closed - Opened by sanchit-saini over 3 years ago
- 13 comments
#28 - Large discrepancy seen when parsing Ensembl GTF vs. GFF3 files
Issue -
State: closed - Opened by mjsteinbaugh over 3 years ago
- 6 comments
#26 - TxDb from NCBI RefSeq GCF_000001405.39_GRCh38.p13 is failing
Issue -
State: closed - Opened by mjsteinbaugh over 3 years ago
- 7 comments
#25 - Fixes to .ALL_SUPPORTED_TX_TABLES to reflect changes at UCSC.
Pull Request -
State: closed - Opened by jmacdon over 3 years ago
- 2 comments
#24 - coverageByTranscript
Pull Request -
State: open - Opened by Roleren almost 4 years ago
#23 - Bug in merge_seqinfo_and_infer_missing_seqlengths for GAlignmentPairs
Issue -
State: closed - Opened by Roleren almost 4 years ago
#22 - makeTxDbFromUCSC fails for hg38
Issue -
State: closed - Opened by Austin-s-h about 4 years ago
- 4 comments
#21 - How to get promoter sequences
Issue -
State: closed - Opened by FritzPeleke about 4 years ago
- 1 comment
#20 - In genes(): Give message about excluding genes
Pull Request -
State: closed - Opened by lshep over 4 years ago
- 1 comment
#19 - coverageByTranscript weights ?
Issue -
State: open - Opened by Roleren over 4 years ago
- 8 comments
Labels: enhancement
#18 - Crash with failed memory allocation/mapping
Issue -
State: closed - Opened by paulmenzel over 4 years ago
- 3 comments
#17 - threeUTRsByTranscript per gene
Issue -
State: closed - Opened by asmagen almost 5 years ago
- 1 comment
#16 - makeTxDbFromUCSC fails with with RMariaDB error
Issue -
State: closed - Opened by balwierz about 5 years ago
- 3 comments
#15 - makeFeatureDbFromUCSC not populating database correctly
Issue -
State: closed - Opened by lshep over 5 years ago
- 6 comments
#14 - Question: error in makeTxDbFromUCSC
Issue -
State: closed - Opened by AlanchenJP over 5 years ago
- 2 comments
#13 - makeTxDbFromGFF not working with GFF3File object
Issue -
State: closed - Opened by FelixErnst over 5 years ago
- 2 comments
#12 - extractTranscriptSeqs fails reconstructing transcripts on minus strand
Issue -
State: closed - Opened by sghignone over 5 years ago
- 2 comments
#11 - makeTxDbFromEnsembl() is broken
Issue -
State: closed - Opened by hpages over 5 years ago
- 2 comments
#10 - pmapFromTranscripts strange behaviour
Issue -
State: open - Opened by Roleren almost 6 years ago
- 12 comments
#9 - Make cdsBy(txdb, by="tx") return the CDS phase
Issue -
State: open - Opened by hpages almost 6 years ago
#8 - How does GenomicFeature calculate 3'UTR?
Issue -
State: closed - Opened by lss1227 about 6 years ago
- 1 comment
#7 - the "phase" metadata column must contain 0, 1, or 2, for all the CDS features
Issue -
State: closed - Opened by AlexWanghaoming about 6 years ago
- 8 comments
#6 - coverageByTranscript, seqlevels
Issue -
State: closed - Opened by Roleren about 6 years ago
- 5 comments
#4 - GenomicFeatures fails to install on CentOS 7.4 w MariaDB
Issue -
State: closed - Opened by mtmorgan over 6 years ago
- 3 comments
#3 - 'names' attribute [211] must be the same length as the vector [209]
Issue -
State: closed - Opened by jamesdalg over 6 years ago
- 2 comments
#2 - extractTranscriptSeqs, needs extra check
Issue -
State: closed - Opened by Roleren over 6 years ago
- 5 comments
#1 - Attach seqlengths to mapToTranscripts() return value
Issue -
State: closed - Opened by lawremi over 6 years ago
- 11 comments