Ecosyste.ms: Issues

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GitHub / Bioconductor/GenomicFeatures issues and pull requests

#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

#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

#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

#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

#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

#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

#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