Showing : gtf • reset
9
votes
9
replies
8.8k
views
extracting gene names, gene id and transcript id
gtf
updated 5.7 years ago by ▴ 70 • written 5.8 years ago by ▴ 670
3
votes
2
replies
2.2k
views
makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
genomicfeatures gtf maketxdbfromgff iGenome
updated 7.5 years ago by 25k • written 7.5 years ago by ▴ 20
3
votes
2
replies
1.1k
views
Import gff from character?
rtracklayer gff gtf import import.gff3
updated 6.9 years ago by 25k • written 6.9 years ago by ▴ 20
3
votes
10
replies
5.8k
views
package to manipulate GTF files
gtf
updated 2.9 years ago by ▴ 80 • written 2.9 years ago by ▴ 10
3
votes
4
replies
2.3k
views
having trouble with dexseq_prepare_annotation.py
dexseq gtf
updated 8.5 years ago by ★ 1.9k • written 8.5 years ago by ▴ 20
2
votes
2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
3.9 years ago keremwai • 0
2
votes
2
replies
818
views
Tximport error (probably annotation lowercase incompatibility)
arabidopsis tximport gtf annotation
updated 5.1 years ago by 42k • written 5.1 years ago by • 0
2
votes
0
replies
1.0k
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 5.1 years ago by • 0 • written 5.1 years ago by 3.9k
2
votes
8
replies
1.8k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 21 months ago by ▴ 10
1
vote
2
replies
1.5k
views
DEXSeq Python script dexseq_prepare_annotation.py unable to process my .gtf file
dexseq python gtf gff3 annotation
4.1 years ago • updated 4.0 years ago Raito92 ▴ 60
1
vote
7
replies
1.1k
views
News: ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
5.6 years ago shepherl 3.9k
1
vote
2
replies
1.2k
views
Create Db for exon starts/ends using rtracklayer
rtracklayer gtf
8.6 years ago Mehmet Ilyas Cosacak • 0
1
vote
6
replies
4.0k
views
Building sqlite file from gtf
gtf sqlite mm9
9.5 years ago • updated 9.4 years ago Patrick Schorderet ▴ 20
1
vote
0
replies
1.4k
views
News: ensembl 91 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit News
6.4 years ago shepherl 3.9k
1
vote
7
replies
3.1k
views
DEXSeq - Where to find and download the appropriate GTF reference file for Python Script
dexseq gtf gff reference genome
updated 7.1 years ago by 66k • written 7.1 years ago by • 0
0
votes
0
replies
642
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
15 months ago yao hua • 0
0
votes
2
replies
2.2k
views
makeTxDbpackage after makeTxDbfromGFF --> Error in spc[[2]] : subscript out of bounds
gtf TxDb maketxdbfromgff
updated 8.9 years ago by 16k • written 8.9 years ago by • 0
0
votes
2
replies
1.8k
views
DEXSeq prepare_annotation.py error
DEXseq gff prepare annotation gtf transcript_id
8.8 years ago arom2 • 0
0
votes
3
replies
2.0k
views
dexseq hg19- create gff
gtf gff
8.7 years ago efratdahan21 • 0
0
votes
7
replies
1.9k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
updated 8.5 years ago by 16k • written 8.5 years ago by • 0
0
votes
0
replies
1.2k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
8.5 years ago Karolin Wiedemann • 0
0
votes
2
replies
2.1k
views
Exporting a GenomicRanges object as GTF/GFF file
genomicranges rtracklayer gtf gff export
7.0 years ago rubi ▴ 110
0
votes
2
replies
1.5k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 6.9 years ago by 42k • written 6.9 years ago by • 0
0
votes
0
replies
994
views
News: ensembl 92 gtfs and fasta twobits have been added to AnnotationHub
ensembl gtf 2bit annotationhub News
6.1 years ago shepherl 3.9k
0
votes
0
replies
962
views
News: ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub ensembl gtf 2bit annotationdata News
5.8 years ago shepherl 3.9k
0
votes
0
replies
1000
views
News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
5.3 years ago shepherl 3.9k
0
votes
0
replies
322
views
help with converting MSTRG tags with isoformswictanalyzer
stringtie IsoformSwitchAnalyzeR pfamAnalyzeR gtf
updated 6 months ago by 66k • written 6 months ago by • 0
0
votes
1
reply
887
views
branchpointer: trouble to read gtf
gtfToExons "Error:subscriptcontainsinvalidnames" gtf branchpointer
updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
28 results • Page 1 of 1
Recent ...
Replies
Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
I don't have an answer to the "why" but maybe a simple reimplemention will do: ```r seqs <- c("ATCATCGTATCAAAGTC", "AAAACGTATCAAAGTC", "TG…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Guido Hooiveld ★ 4.0k
After checking `?DESeqDataSetFromMatrix` note this information: arguments provided to SummarizedExperiment including rowRanges and met…
Answer: Error in gseDO function by Guido Hooiveld ★ 4.0k
Yes, you are missing something. :-) For a GSEA you will need to use as input all genes that you are analyzing; these genes should be ran…
Comment: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Comment: conumee with Infinium MethylationEPIC v2.0 by sgomez • 0
Hi Max, Could you try this? https://support.bioconductor.org/p/9136138/#9136840
Votes
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
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