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read counting
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reset
4
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Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
summarizeoverlaps
rnaseq
bplapply
rangedsummarizedexperiment
read counting
8.7 years ago
ErickF
▴ 40
3
votes
2
replies
1.2k
views
counting the sequencing reads in 10kb regions on a genome-wide scale
read counting
CNV
rsamtools
updated 7.0 years ago by
James W. MacDonald
68k • written 7.0 years ago by
Bogdan
▴ 670
1
vote
12
replies
4.4k
views
Problem with summarizeOverlaps function
genomicalignments
read counting
9.5 years ago
kgorczak
▴ 10
1
vote
4
replies
2.4k
views
Gviz sashimi read count
Gviz
sashimi
sashimi plots
read counting
bam
updated 8.0 years ago by
Robert Ivanek
▴ 750 • written 8.0 years ago by
bernt.popp
• 0
1
vote
4
replies
2.5k
views
DiffBind error with dba.count after update
diffbind
read counting
warning message
chromatin
atac-seq
updated 7.3 years ago by
Gord Brown
▴ 670 • written 7.4 years ago by
tgjohnst
• 0
0
votes
1
reply
1.4k
views
featureCounts : limits on multioverlap (option -O)
featurecounts
read counting
updated 7.1 years ago by
Gordon Smyth
52k • written 7.1 years ago by
marc.gabriel.01
• 0
6 results • Page
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Answer: Use of org.Rn.eg.db with GRCr8 reference genome
by
James W. MacDonald
68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column
by
Erika
• 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping
by
James W. MacDonald
68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question?
by
DavideSant
• 0
Thank you, this was super useful!
Comment: Error in retrieving clinical data
by
silickas
• 0
Thank you for the reply. I will try to do that next time. This time instead, I used the GenomicDataCommons package to download clinical dat…
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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