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Creating a DESeqDataSet from a RangedSummarizedExperiment - where is the design parameter in RangedSummarizedExperiment
SRA
DESeq2
2.9 years ago
Serge
• 0
0
votes
0
replies
911
views
Problem for Splitting reverse and forward reading in my RNA-seq
RNA-seq
SRA
reverse reads
forward reads
5.8 years ago
modarzi
▴ 10
2
votes
1
reply
1.3k
views
Uniting SRA Data into a single file
R
fastq
SRA
sradb
updated 7.5 years ago by
Martin Morgan
25k • written 7.5 years ago by
grecoandreauni
• 0
0
votes
3
replies
3.2k
views
download SRR*.lite.sra files using fastq-dump command
sra
chipseqDB
fastq-dump
.lite.sra
updated 7.6 years ago by
James W. MacDonald
65k • written 7.6 years ago by
xhe764
• 0
0
votes
0
replies
1.4k
views
Search SRA based on BioSample Attributes
ncbi
sra
search
8.3 years ago
massacomgrao
• 0
6
votes
1
reply
3.9k
views
Tutorial:
Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
rnaseq
biocparallel
workflows
sra
Tutorial
8.8 years ago
Sean Davis
21k
6 results • Page
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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