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Bioconductor
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GenomicFeatures
Query the gene models of a given organism/assembly
https://bioconductor.org/packages/GenomicFeatures
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`makeTxDbFromEnsembl` no longer connects to the right Ensembl database for Homo sapiens
#69
divibisan
opened
1 month ago
0
How to import pseudogenes from GFF3 file as GRanges object?
#68
zhewa
opened
7 months ago
0
GenomicFeatures:::load_package_gracefully apparently fails on BBS
#67
FelixErnst
closed
7 months ago
2
Feature Request: Implementation of getTerminatorSeq() Function
#66
JavierMenRev
closed
9 months ago
6
How to make a TxDb object for the T2T-CHM13v2.0 genome (telomere to telomere Human genome)
#65
hpages
closed
7 months ago
0
Installation requires vctrs (≥ 0.6.0)
#64
amitfrishberg
closed
1 year ago
4
GenomicFeature error with mm10
#63
MurliNair
closed
1 year ago
7
makeTxDbFromUCSC failed for susScr11
#62
sinnis007
closed
1 year ago
3
makeTxDbFromUCSC failed for mm9
#61
Moonriver1988
closed
1 year ago
4
Extracting exons result is different from manual extraction
#60
gernophil
closed
1 year ago
5
fiveUTRsByTranscript() and threeUTRsByTranscript() give incorrect UTRs
#59
a92932000
closed
1 year ago
3
installation issue
#58
LliliansCalvo
closed
1 year ago
1
`makeTxDbFromBiomart()` on the Ensembl archive version failed
#57
timedreamer
closed
9 months ago
14
`makeTxDbFromGFF` fails with (bacterial) genome GTF files from NCBI
#56
m-jahn
closed
9 months ago
5
Add 'genome' argument to makeTxDbFromGFF()
#55
hpages
closed
7 months ago
3
mapToTranscripts reports incorrect regions when supplied GRangesList containing some empty transcripts
#54
kriemo
opened
1 year ago
0
Create custom TxDb Package from NCBI GFF file
#53
sopeadeniji
closed
1 year ago
2
makeTxDbPackageFromUCSC failed
#52
haowulab
closed
1 year ago
3
makeTxDbFromGFF fails, possibly due to download.file / restfulr?
#51
AMChalkie
closed
1 year ago
3
makeTxDbFromUCSC fails to connect to UCSC server
#50
ameliaregina
closed
2 years ago
6
makeTxDbFromEnsembl for Ensembl AnnotationHub objects?
#49
mschubert
closed
2 years ago
1
makeTxDbFromBiomart error when querying fungi hosts
#48
LiNk-NY
closed
2 years ago
6
Find coordinates of all known transcription start and termination sites (TSS TTS) for a gene
#47
pgupta3005
closed
2 years ago
4
How to find the reference to an organism in the organism database?
#46
prmunn
closed
2 years ago
2
ExtractTranscriptSeqs extracted sequences with non-base
#45
lbwfff
closed
2 years ago
1
threeUTRsByTranscript() and fiveUTRsByTranscript() are not working correctly on minus strand
#44
anmej
closed
1 year ago
1
exonsBy Option to Resize Exons for Splicing Donor and Acceptor Regions
#43
DarioS
closed
2 years ago
3
error unknown
#41
under-score
closed
2 years ago
3
promoters() returns out of range indicies
#40
cmatKhan
closed
2 years ago
3
transition the package to useEnsembl
#39
LiNk-NY
closed
2 years ago
0
makeTxDbFromUCSC failing on check of txtable
#38
jmacdon
closed
2 years ago
2
GENE IDs are not loaded from UCSC tables using makeTxDbPackageFromUCSC
#37
farshadf
closed
2 years ago
6
makeTxDbFromGFF() how to handle entries lacking or duplicated "transcript_id" attribute
#36
madzafv
closed
2 years ago
2
Why 'downstream' is set to 200 by default in getPromoterSeq()
#35
hpages
closed
2 years ago
4
`makeTxDbFromUCSC` fails with `!anyNA(m32) is not TRUE`
#34
edikedik
closed
3 years ago
1
protein_coding_gene not recognized as valid gene feature
#33
cmatKhan
closed
3 years ago
1
Fail to add stop_codon through makeTxDbFromGRanges
#32
ggoodstudydaydayup
closed
3 years ago
5
Get gene_name column from GENCODE GTF?
#31
Zepeng-Mu
closed
3 years ago
1
Unable to parse bacterial GFF files
#30
jambler24
closed
2 years ago
1
Affected changes from the new UCSC Table Query interface of rtracklayer package
#29
sanchit-saini
closed
3 years ago
13
Large discrepancy seen when parsing Ensembl GTF vs. GFF3 files
#28
mjsteinbaugh
closed
3 years ago
6
TxDb from NCBI RefSeq GCF_000001405.39_GRCh38.p13 is failing
#26
mjsteinbaugh
closed
1 year ago
7
Fixes to .ALL_SUPPORTED_TX_TABLES to reflect changes at UCSC.
#25
jmacdon
closed
4 years ago
2
coverageByTranscript
#24
Roleren
opened
4 years ago
0
Bug in merge_seqinfo_and_infer_missing_seqlengths for GAlignmentPairs
#23
Roleren
closed
4 years ago
0
makeTxDbFromUCSC fails for hg38
#22
Austin-s-h
closed
4 years ago
4
How to get promoter sequences
#21
FritzPeleke
closed
4 years ago
1
In genes(): Give message about excluding genes
#20
lshep
closed
4 years ago
1
coverageByTranscript weights ?
#19
Roleren
opened
4 years ago
8
Crash with failed memory allocation/mapping
#18
paulmenzel
closed
7 months ago
3
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