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DEseq
•
reset
3
votes
2
replies
305
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq
DESeq2
6 months ago
manwar
• 0
2
votes
4
replies
2.6k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
updated 11 months ago by
Nicola
• 0 • written 2.8 years ago by
krunal.24.6
▴ 10
2
votes
1
reply
470
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 8 months ago by
swbarnes2
★ 1.2k • written 8 months ago by
Hicham
• 0
1
vote
2
replies
341
views
Deseq2 with imbalanced design
Deseq
10 months ago
Alex
• 0
1
vote
1
reply
181
views
How to design multifactor DESEQ2 formula?
DESEQ
DESEQ2
updated 5 months ago by
ATpoint
★ 2.1k • written 5 months ago by
barrypraveen
• 0
1
vote
1
reply
291
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 7 months ago by
Michael Love
39k • written 7 months ago by
stew
• 0
1
vote
5
replies
602
views
Potential outlier/high variance
deseq
DESeq2
updated 9 months ago by
Michael Love
39k • written 10 months ago by
Amali Thrimawithana
• 0
1
vote
5
replies
425
views
Error in DEseq
DEseq
RNASeqData
updated 8 months ago by
ATpoint
★ 2.1k • written 8 months ago by
Sanatan
• 0
0
votes
1
reply
2.3k
views
voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization
graph
limma
convert
edgeR
DESeq
Rsubread
Normalization
graph
limma
convert
updated 5 weeks ago by
Gordon Smyth
47k • written 10.7 years ago by
Kasper Daniel Hansen
6.5k
0
votes
1
reply
100
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 10 days ago by
Michael Love
39k • written 12 days ago by
m-bihie
▴ 10
0
votes
1
reply
125
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 20 days ago by
Dario Strbenac
★ 1.5k • written 22 days ago by
Hicham
• 0
0
votes
2
replies
770
views
suggestions/comments on DESeq transcript wise analysis
convert
DESeq
convert
DESeq
written 11.0 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
12 results • Page
1 of 1
Recent ...
Replies
Comment: TCGA: clinical data and expression data
by
sharifnstu1203002m
• 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Jonathan Göke
▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
by
Gordon Smyth
47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user)
by
lalanis1
• 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma
by
Gordon Smyth
47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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to
James W. MacDonald
62k
Teacher
to
Michael Love
39k
Popular Question
to
Gordon Smyth
47k
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to
Bogdan
▴ 660
Popular Question
to
Martin Morgan
25k
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