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RNASeq123
•
reset
12
votes
4
replies
4.4k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 5.3 years ago by
Gordon Smyth
50k • written 6.9 years ago by
wd
▴ 30
1
vote
3
replies
4.4k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 3.3 years ago by
mmicky5050
• 0
0
votes
3
replies
829
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 16 months ago by
Michael Love
41k • written 16 months ago by
irish.prg
• 0
2
votes
5
replies
1.0k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR
RNAseq123
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
Istvan Albert
▴ 50
0
votes
1
reply
816
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 2.8 years ago by
Kevin Blighe
★ 3.9k • written 2.8 years ago by
kusum
• 0
1
vote
2
replies
186
views
Improving the design matrices vignette in RNAseq123
RNAseq123
14 days ago • updated 12 hours ago
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
1.5k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 18 months ago by
James W. MacDonald
65k • written 18 months ago by
Mohamed
▴ 30
2
votes
1
reply
1.0k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
Mikołaj Mierzejewski
• 0
0
votes
2
replies
543
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
14 months ago
fatemeh.peimani
• 0
1
vote
6
replies
3.2k
views
KEGG enrichment analysis for non model organism
RNAseq123
17 months ago
afsanarupa1
• 0
1
vote
1
reply
335
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
kaurprab
• 0
5
votes
6
replies
2.5k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
2.1 years ago
Alan
• 0
1
vote
1
reply
1.3k
views
featureCounts running too long
RNAseq123
updated 3 months ago by
difraiadomenico
• 0 • written 3.2 years ago by
demirkalecy
▴ 10
0
votes
0
replies
552
views
Plotting a line plot for genes across 4-species
RNAseq123
21 months ago
Mohamed
▴ 30
0
votes
0
replies
511
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
3.2 years ago
rpokhre2
• 0
1
vote
1
reply
713
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 20 months ago by
ATpoint
★ 4.1k • written 20 months ago by
Mohamed
▴ 30
16 results • Page
1 of 1
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Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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Malcolm Cook
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Gordon Smyth
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priyanka.m
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Vincent J. Carey, Jr.
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