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Showing :
gtf
•
reset
9
votes
9
replies
8.6k
views
extracting gene names, gene id and transcript id
gtf
updated 5.6 years ago by
lee.s
▴ 70 • written 5.6 years ago by
Bogdan
▴ 670
3
votes
10
replies
5.5k
views
package to manipulate GTF files
gtf
updated 2.8 years ago by
Konstantinos Yeles
▴ 80 • written 2.8 years ago by
pcantalupo
▴ 10
1
vote
6
replies
3.9k
views
Building sqlite file from gtf
gtf
sqlite
mm9
9.3 years ago
Patrick Schorderet
▴ 20
1
vote
7
replies
3.0k
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
3
votes
4
replies
2.2k
views
having trouble with dexseq_prepare_annotation.py
dexseq
gtf
updated 8.4 years ago by
Alejandro Reyes
★ 1.9k • written 8.4 years ago by
vakul.mohanty
▴ 10
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
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 7.4 years ago by
Marlin
▴ 20
0
votes
2
replies
2.1k
views
Exporting a GenomicRanges object as GTF/GFF file
genomicranges
rtracklayer
gtf
gff
export
6.8 years ago
rubi
▴ 110
0
votes
3
replies
2.0k
views
dexseq hg19- create gff
gtf
gff
8.6 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
2
replies
1.7k
views
DEXSeq prepare_annotation.py error
DEXseq
gff
prepare annotation
gtf
transcript_id
8.7 years ago
arom2
• 0
2
votes
8
replies
1.7k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing
RNASeq
IsoformSwitchAnalyzeR
gtf
written 20 months ago by
bpshtiwan
▴ 10
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
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 • updated 3.9 years ago
Raito92
▴ 60
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
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
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
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
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
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
0
votes
0
replies
970
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
2
votes
0
replies
969
views
News:
ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
updated 4.9 years ago by
nguyenlieuduoc
• 0 • written 5.0 years ago by
shepherl
3.8k
0
votes
0
replies
963
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
935
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
1
reply
843
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
2
votes
2
replies
799
views
Tximport error (probably annotation lowercase incompatibility)
arabidopsis
tximport
gtf
annotation
updated 5.0 years ago by
Michael Love
41k • written 5.0 years ago by
francoagp
• 0
0
votes
0
replies
607
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
14 months ago
yao hua
• 0
0
votes
0
replies
257
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
28 results • Page
1 of 1
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Replies
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Comment: Estimating Cell Counts for EPIC V2 array data
by
normawiedman059
• 0
0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Votes
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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