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Tximport
•
reset
0
votes
5
replies
10k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 10 months ago by
Eva
• 0 • written 8.3 years ago by
ctl
• 0
1
vote
2
replies
2.3k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 7 months ago by
rodrigo.duarte88
▴ 40 • written 5.2 years ago by
mohamedrefaat.1.1992
• 0
6
votes
7
replies
3.2k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR
tximport
differential expression
updated 23 days ago by
Gordon Smyth
52k • written 4.7 years ago by
hollandademello
▴ 20
1
vote
2
replies
485
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
6 weeks ago
georgii.vdovin
• 0
0
votes
2
replies
419
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
oguzhankaraosmanoglu
• 0
0
votes
11
replies
608
views
Problems with oarfish + tximport + swish
fishpond
tximport
tximeta
updated 3 days ago by
Im
• 0 • written 7 days ago by
brown.annaleigh
• 0
0
votes
2
replies
631
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 10 months ago by
Michael Love
43k • written 10 months ago by
SG
• 0
2
votes
5
replies
2.0k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 11 months ago by
Michael Love
43k • written 2.1 years ago by
kiqbal
• 0
0
votes
2
replies
447
views
tximport data import
tximport
updated 4 months ago by
Michael Love
43k • written 4 months ago by
rodongo
• 0
0
votes
2
replies
954
views
tximport error in reading salmon output files?
tximport
tximportData
updated 11 months ago by
Matteo
• 0 • written 19 months ago by
barrypraveen
• 0
2
votes
1
reply
535
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 10 months ago by
ATpoint
★ 4.6k • written 10 months ago by
hemantcnaik
• 0
2
votes
3
replies
1.8k
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
written 2.3 years ago by
L
▴ 50
6
votes
10
replies
2.8k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 9 months ago by
i.atanasoai
• 0 • written 23 months ago by
mohammedtoufiq91
▴ 10
0
votes
4
replies
639
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
7 months ago
JG13
• 0
0
votes
2
replies
588
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
9 months ago
Marianna
▴ 20
1
vote
2
replies
833
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2
tximport
5 months ago
grothmn
• 0
4
votes
5
replies
684
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
11 weeks ago
LuciaNhu
• 0
17 results • Page
1 of 1
Recent ...
Replies
Comment: Rain error: invalid annotation of time points
by
Dominik
• 0
Hi, I kept running into the same issue until I double checked their help and understood, that columns and rows have to be designed in anoth…
Answer: How to generate circular cnetplot and color nodes and edges in the same plot ?
by
Guido Hooiveld
★ 4.1k
Since the release of `enrichplot` of October 2024, the code of the function `cnetplot` has been completely rewritten by Guangchuang in orde…
Comment: CUT&Tag differential peak analysis using Diffbind, with pre-calculated normaliza
by
mec25
• 0
I am unable to find the math behind the dba.normalize(), for instance when the E-coli fraction is used is the signal mutliplied by the fact…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA?
by
Quang NN
▴ 10
Thank you so much for taking time to provide this clarification!
Comment: How can I generate a heatmap and clustering of differentially expressed genes in
by
Renuka
• 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Votes
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
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