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GTF
•
reset
9
votes
9
replies
8.6k
views
extracting gene names, gene id and transcript id
gtf
updated 5.7 years ago by
lee.s
▴ 70 • written 5.7 years ago by
Bogdan
▴ 670
3
votes
2
replies
2.2k
views
makeTxDbFromGFF drops genes which have multiple chromosome locations. (with iGenome GTF)
genomicfeatures
gtf
maketxdbfromgff
iGenome
updated 7.4 years ago by
Martin Morgan
25k • written 7.5 years ago by
Marlin
▴ 20
3
votes
2
replies
1.1k
views
Import gff from character?
rtracklayer
gff
gtf
import
import.gff3
updated 6.8 years ago by
Martin Morgan
25k • written 6.8 years ago by
Marlin
▴ 20
3
votes
10
replies
5.6k
views
package to manipulate GTF files
gtf
updated 2.8 years ago by
Konstantinos Yeles
▴ 80 • written 2.8 years ago by
pcantalupo
▴ 10
3
votes
4
replies
2.2k
views
having trouble with dexseq_prepare_annotation.py
dexseq
gtf
updated 8.5 years ago by
Alejandro Reyes
★ 1.9k • written 8.5 years ago by
vakul.mohanty
▴ 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
2
votes
2
replies
800
views
Tximport error (probably annotation lowercase incompatibility)
arabidopsis
tximport
gtf
annotation
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
francoagp
• 0
2
votes
0
replies
977
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
nguyenlieuduoc
• 0 • written 5.0 years ago by
shepherl
3.8k
2
votes
8
replies
1.7k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing
RNASeq
IsoformSwitchAnalyzeR
gtf
written 20 months ago by
bpshtiwan
▴ 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
4.0 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
5.5 years ago
shepherl
3.8k
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
1
vote
6
replies
3.9k
views
Building sqlite file from gtf
gtf
sqlite
mm9
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
6.3 years ago
shepherl
3.8k
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
James W. MacDonald
65k • written 7.0 years ago by
greg.mulhearn
• 0
0
votes
0
replies
613
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
14 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 8.8 years ago by
Hervé Pagès
16k • written 8.8 years ago by
yacine.badis
• 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
3
replies
2.0k
views
dexseq hg19- create gff
gtf
gff
8.7 years ago
efratdahan21
• 0
0
votes
7
replies
1.8k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures
maketxdbfromgff
tx_type
gtf
updated 8.4 years ago by
Hervé Pagès
16k • written 8.4 years ago by
Karolin Wiedemann
• 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
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
0
votes
2
replies
1.5k
views
makeTxDbFromGFF Error due to incompatible seqnames
summarizedexperiment
TxDb
gtf
genomicfeatures
updated 6.8 years ago by
Michael Love
41k • written 6.8 years ago by
filipeje
• 0
0
votes
0
replies
973
views
News:
ensembl 92 gtfs and fasta twobits have been added to AnnotationHub
ensembl
gtf
2bit
annotationhub
News
6.0 years ago
shepherl
3.8k
0
votes
0
replies
940
views
News:
ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
ensembl
gtf
2bit
annotationdata
News
5.7 years ago
shepherl
3.8k
0
votes
0
replies
974
views
News:
ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
annotationdata
ensembl
gtf
2bit
News
5.2 years ago
shepherl
3.8k
0
votes
0
replies
267
views
help with converting MSTRG tags with isoformswictanalyzer
stringtie
IsoformSwitchAnalyzeR
pfamAnalyzeR
gtf
updated 4 months ago by
James W. MacDonald
65k • written 4 months ago by
sumitra.20
• 0
0
votes
1
reply
851
views
branchpointer: trouble to read gtf
gtfToExons
"Error:subscriptcontainsinvalidnames"
gtf
branchpointer
updated 2.6 years ago by
b.signal
• 0 • written 2.6 years ago by
frank.maiwald
• 0
28 results • Page
1 of 1
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Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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