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tximport
•
reset
0
votes
4
replies
491
views
Using tximport for kallisto aligned TOIL data
kallisto
tximport
TOIL
15 days ago • updated 5 days ago
Nicholas
• 0
0
votes
11
replies
807
views
Problems with oarfish + tximport + swish
fishpond
tximport
tximeta
updated 8 weeks ago by
Im
• 0 • written 9 weeks ago by
brown.annaleigh
• 0
1
vote
2
replies
657
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
3 months ago
georgii.vdovin
• 0
4
votes
5
replies
871
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
4 months ago
LuciaNhu
• 0
0
votes
2
replies
490
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 5 months ago by
Michael Love
43k • written 5 months ago by
oguzhankaraosmanoglu
• 0
0
votes
2
replies
497
views
tximport data import
tximport
updated 6 months ago by
Michael Love
43k • written 6 months ago by
rodongo
• 0
1
vote
2
replies
945
views
How to use specific size factors and average transcript lengths from tximport in DESeq2?
DESeq2
tximport
7 months ago
grothmn
• 0
1
vote
2
replies
2.4k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 9 months ago by
rodrigo.duarte88
▴ 40 • written 5.4 years ago by
mohamedrefaat.1.1992
• 0
0
votes
4
replies
706
views
Create count matrix from multible quant sf files from different directories
tximportData
tximport
salmon
9 months ago
JG13
• 0
0
votes
2
replies
662
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
11 months ago
Marianna
▴ 20
0
votes
2
replies
712
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 12 months ago by
Michael Love
43k • written 12 months ago by
SG
• 0
6
votes
10
replies
3.2k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 11 months ago by
i.atanasoai
• 0 • written 2.1 years ago by
mohammedtoufiq91
▴ 10
2
votes
3
replies
1.9k
views
How to convert transcript counts to gene counts in R?
DESeq2
tximport
written 2.4 years ago by
L
▴ 50
6
votes
7
replies
3.4k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR
tximport
differential expression
updated 11 weeks ago by
Gordon Smyth
52k • written 4.8 years ago by
hollandademello
▴ 20
14 results • Page
1 of 1
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Replies
Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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