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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
863
views
Is possible to use NOISeq with counts from RSubread?
noiseq
rsubread
tophat
bowtie
bowtie2
5.0 years ago
Marcelo Laia
▴ 450
0
votes
1
reply
911
views
Filtering Tophat/cufflinks data for GSEA with topGO
topGO
tophat
kolmogorov-smirnov test
updated 6.9 years ago by
James W. MacDonald
66k • written 6.9 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 7.6 years ago by
Thomas Girke
★ 1.7k • written 7.6 years ago by
abass.conteh
• 0
2
votes
9
replies
7.6k
views
Multiple alignments (multi-mapped reads) and DESeq/edgeR pipeline
deseq
deseq2
edger
tophat
bowtie
9.0 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 9.6 years ago by
Dan Tenenbaum
★ 8.2k • written 9.6 years ago by
alejandro.colaneri
▴ 20
6 results • Page
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Comment: How to compare subset of samples from VCF files
by
Gordon Smyth
50k
Welcome to Bioconductor support. Did you know that you can delete your old postings if they haven't received an answer yet? Instead of ap…
Comment: How to compare subset of samples from VCF files
by
Marco
• 0
Here's the vcf file as code block ``` ##fileformat=VCFv4.2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth"> ##FOR…
Comment: Gviz and custom database
by
James W. MacDonald
66k
The vignette for `Gviz` says you can use a `DNAStringSet`, generated using `Biostrings`. Have you tried that?
Comment: Gviz and custom database
by
luigi.faino
• 0
Dear, this is not what I need. I need to transform a fasta sequence in a genome track usable in Gviz. L
Answer: Gviz and custom database
by
James W. MacDonald
66k
https://bioconductor.org/packages/release/bioc/vignettes/txdbmaker/inst/doc/txdbmaker.html
Votes
Answer: makeExampleDESeqDataSet using pilot data
Answer: Checking/updating package versions
Answer: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
convert data frame of Entrez IDs to Gene Symbols
Answer: LRT, pairwise comparisons and p-value adjustment
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