Showing : GTF • reset
0
votes
0
replies
283
views
help with converting MSTRG tags with isoformswictanalyzer
stringtie IsoformSwitchAnalyzeR pfamAnalyzeR gtf
updated 5 months ago by 65k • written 5 months ago by • 0
0
votes
0
replies
625
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
14 months ago yao hua • 0
2
votes
8
replies
1.7k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 21 months ago by ▴ 10
0
votes
1
reply
865
views
branchpointer: trouble to read gtf
gtfToExons "Error:subscriptcontainsinvalidnames" gtf branchpointer
updated 2.6 years ago by • 0 • written 2.6 years ago by • 0
3
votes
10
replies
5.7k
views
package to manipulate GTF files
gtf
updated 2.8 years ago by ▴ 80 • written 2.8 years ago by ▴ 10
2
votes
2
replies
1.1k
views
Tximport missing values for group summarizing counts
tximport rat reference GTF salmon
3.8 years ago keremwai • 0
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
4.0 years ago Raito92 ▴ 60
2
votes
0
replies
985
views
News: ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata annotationhub ensembl gtf 2bit News
updated 5.0 years ago by • 0 • written 5.0 years ago by 3.9k
2
votes
2
replies
809
views
Tximport error (probably annotation lowercase incompatibility)
arabidopsis tximport gtf annotation
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
0
votes
0
replies
980
views
News: ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub annotationdata ensembl gtf 2bit News
5.2 years ago shepherl 3.9k
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
9
votes
9
replies
8.7k
views
extracting gene names, gene id and transcript id
gtf
updated 5.7 years ago by ▴ 70 • written 5.7 years ago by ▴ 670
0
votes
0
replies
948
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
982
views
News: ensembl 92 gtfs and fasta twobits have been added to AnnotationHub
ensembl gtf 2bit annotationhub News
6.0 years ago shepherl 3.9k
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
0
votes
2
replies
1.5k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment TxDb gtf genomicfeatures
updated 6.8 years ago by 41k • written 6.8 years ago by • 0
3
votes
2
replies
1.1k
views
Import gff from character?
rtracklayer gff gtf import import.gff3
updated 6.8 years ago by 25k • written 6.8 years ago by ▴ 20
0
votes
2
replies
2.1k
views
Exporting a GenomicRanges object as GTF/GFF file
genomicranges rtracklayer gtf gff export
6.9 years ago rubi ▴ 110
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 7.0 years ago by 65k • written 7.0 years ago by • 0
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
0
votes
7
replies
1.9k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
updated 8.4 years ago by 16k • written 8.4 years ago by • 0
0
votes
0
replies
1.2k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
8.4 years ago Karolin Wiedemann • 0
3
votes
4
replies
2.2k
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
1
vote
2
replies
1.2k
views
Create Db for exon starts/ends using rtracklayer
rtracklayer gtf
8.5 years ago Mehmet Ilyas Cosacak • 0
0
votes
3
replies
2.0k
views
dexseq hg19- create gff
gtf gff
8.7 years ago efratdahan21 • 0
0
votes
2
replies
1.8k
views
DEXSeq prepare_annotation.py error
DEXseq gff prepare annotation gtf transcript_id
8.7 years ago arom2 • 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
1
vote
6
replies
4.0k
views
Building sqlite file from gtf
gtf sqlite mm9
9.4 years ago Patrick Schorderet ▴ 20
28 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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