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Tximport
•
reset
1
vote
2
replies
176
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
1 day ago
georgii.vdovin
• 0
4
votes
5
replies
609
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
5 weeks ago
LuciaNhu
• 0
0
votes
2
replies
369
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 10 weeks ago by
Michael Love
43k • written 10 weeks ago by
oguzhankaraosmanoglu
• 0
0
votes
2
replies
405
views
tximport data import
tximport
updated 3 months ago by
Michael Love
43k • written 3 months ago by
rodongo
• 0
1
vote
2
replies
777
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2
tximport
4 months ago
grothmn
• 0
1
vote
2
replies
2.2k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 6 months ago by
rodrigo.duarte88
▴ 40 • written 5.1 years ago by
mohamedrefaat.1.1992
• 0
0
votes
4
replies
595
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
6 months ago
JG13
• 0
0
votes
2
replies
537
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
8 months ago
Marianna
▴ 20
0
votes
2
replies
577
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 8 months ago by
Michael Love
43k • written 8 months ago by
SG
• 0
2
votes
1
reply
495
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 9 months ago by
ATpoint
★ 4.6k • written 9 months ago by
hemantcnaik
• 0
2
votes
3
replies
2.4k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR
tximport
RNASeq
DESeq2
updated 11 months ago by
swbarnes2
★ 1.4k • written 12 months ago by
Bo
• 0
0
votes
1
reply
700
views
tximport error with rsem files
rsem
tximport
updated 12 months ago by
ATpoint
★ 4.6k • written 12 months ago by
apolitics
• 0
0
votes
2
replies
916
views
tximport error in reading salmon output files?
tximport
tximportData
updated 10 months ago by
Matteo
• 0 • written 18 months ago by
barrypraveen
• 0
6
votes
10
replies
2.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 7 months ago by
i.atanasoai
• 0 • written 22 months ago by
mohammedtoufiq91
▴ 10
2
votes
5
replies
1.9k
views
Normalizing Salmon output count data matrix using DESeq2
DESeq2
tximport
counts
Salmon
updated 9 months ago by
Michael Love
43k • written 23 months ago by
kiqbal
• 0
2
votes
3
replies
1.7k
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
written 2.1 years ago by
L
▴ 50
0
votes
5
replies
10k
views
tximport all(file.exists(files)) is not TRUE
bioconductor
tximport
rnaseq
R
updated 8 months ago by
Eva
• 0 • written 8.2 years ago by
ctl
• 0
17 results • Page
1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library
by
María Calvo
• 0
Hello Mercedeh, excuse me for not explaining it adecuately, Im using the "Part3 - Identify significant miRNA mRNA relationships for 2 time …
Comment: Need new version : tx2gene.gencode.v47.csv
by
Guido Hooiveld
★ 4.1k
Assuming that you would like to import the results from `salmon`, it is highly recommended to now use `tximeta`. By doing so, all required …
Comment: Help using rtracklayer for gene ID extraction
by
Aichatou
• 0
Hello, Please disregard the previous post. it's working now, i think. I am able to create the txdb object but I can't see all the other inf…
Comment: p value is 0, padj is 0
by
Wirayatida
• 0
Than you so much. My counts are 47,37 and 72 for mock. The treatment is 8153, 6723 and 8024.
Comment: p value is 0, padj is 0
by
Wirayatida
• 0
Thank you so much for your information. I understand it.
Votes
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
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