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tophat
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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
0
votes
1
reply
823
views
Is possible to use NOISeq with counts from RSubread?
noiseq
rsubread
tophat
bowtie
bowtie2
4.9 years ago
Marcelo Laia
▴ 450
0
votes
1
reply
894
views
Filtering Tophat/cufflinks data for GSEA with topGO
topGO
tophat
kolmogorov-smirnov test
updated 6.8 years ago by
James W. MacDonald
65k • written 6.8 years ago by
aaronrosenstein
• 0
2
votes
3
replies
2.1k
views
SystemPipeR: alignments with ambiguous pairing were dumped.
R
rnaseq
tophat
summarizeoverlaps
systempiper
updated 7.5 years ago by
Thomas Girke
★ 1.7k • written 7.5 years ago by
abass.conteh
• 0
2
votes
9
replies
7.5k
views
Multiple alignments (multi-mapped reads) and DESeq/edgeR pipeline
deseq
deseq2
edger
tophat
bowtie
8.9 years ago
ysdel
▴ 40
0
votes
3
replies
2.4k
views
Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq
summarizeOverlaps
deseq2
tophat
genomicalignments
updated 9.5 years ago by
Dan Tenenbaum
★ 8.2k • written 9.5 years ago by
alejandro.colaneri
▴ 20
6 results • Page
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Answer: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
> When I search camera limma on pubmed, I found 2 papers I am unclear what point you are trying to make. limma's camera method has been fo…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function?
by
Henrik Bengtsson
★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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