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RNAseq123
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325
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma
RNAseq123
6 months ago
tim.meese
• 0
1
vote
2
replies
525
views
Improving the design matrices vignette in RNAseq123
RNAseq123
11 months ago
Lluís Revilla Sancho
▴ 760
1
vote
1
reply
764
views
Differential gene expression analysis
RNASeqData
RNAseq123
updated 16 months ago by
ATpoint
★ 4.8k • written 16 months ago by
kaurprab
• 0
0
votes
2
replies
951
views
Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
DESeq2
RNAseq123
2.2 years ago
fatemeh.peimani
• 0
0
votes
3
replies
1.4k
views
DESeq2 Statistic - Padj NA
DESeq2
RNAseq123
rnaseq
deseq2
metatranscriptomic
updated 2.3 years ago by
Michael Love
43k • written 2.3 years ago by
irish.prg
• 0
1
vote
6
replies
5.5k
views
KEGG enrichment analysis for non model organism
RNAseq123
2.3 years ago
afsanarupa1
• 0
2
votes
5
replies
1.5k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR
RNAseq123
updated 2.4 years ago by
Gordon Smyth
52k • written 2.4 years ago by
Istvan Albert
▴ 50
0
votes
1
reply
2.4k
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123
VariantFiltering
Alignment
VariantAnnotation
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Mohamed
▴ 30
1
vote
1
reply
1.0k
views
Confused about design for RNA seq experiment
RNAseq
ExperimentData
RNAseq123
RNA
ExperimentalDesign
updated 2.6 years ago by
ATpoint
★ 4.8k • written 2.6 years ago by
Mohamed
▴ 30
0
votes
0
replies
788
views
Plotting a line plot for genes across 4-species
RNAseq123
2.7 years ago
Mohamed
▴ 30
2
votes
1
reply
1.4k
views
Error in RNAseq123 analysis, unexpected symbol.
RNAseq123
Rna
updated 2.8 years ago by
Gordon Smyth
52k • written 2.8 years ago by
Mikołaj Mierzejewski
• 0
5
votes
6
replies
3.8k
views
Large difference in PCA plot based on LCPM (log counts per million) and VST (variance stabilizing transformations)
PCAtools
edgeR
pcaExplorer
RNASeq
RNAseq123
3.0 years ago
Alan
• 0
0
votes
1
reply
1.1k
views
python and R
snpeff
python
tophat
r
RNAseq123
updated 3.7 years ago by
Kevin Blighe
★ 4.0k • written 3.7 years ago by
kusum
• 0
1
vote
1
reply
2.0k
views
featureCounts running too long
RNAseq123
updated 14 months ago by
difraiadomenico
• 0 • written 4.1 years ago by
demirkalecy
▴ 10
0
votes
0
replies
739
views
Circular RNA
CircularRNA
RNASeq
RNAseq123
4.2 years ago
rpokhre2
• 0
1
vote
3
replies
5.9k
views
Using TMM normalized counts in Deseq2
RNAseq123
written 4.3 years ago by
mmicky5050
• 0
12
votes
4
replies
5.0k
views
differential expression analysis of htseq data with edgeR/voom
voom
htseq
edgeR
limma
RNASeq123
updated 6.3 years ago by
Gordon Smyth
52k • written 7.8 years ago by
wd
▴ 30
17 results • Page
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Replies
Answer: fast apply on RleList
by
story.benjamin
▴ 20
solved with viewApply (code is simplified below) test.split <- split(test.gr,seqnames(test.gr)) final.stats <- mclapply(uniqu…
Comment: fast apply on RleList
by
story.benjamin
▴ 20
Hi James, thanks for the reply. I ultimately figured it out ... viewApply showed a massive speed increase for me (see other answer) - I was…
Answer: fast apply on RleList
by
James W. MacDonald
68k
There is already a 'mean' function that will dispatch on an `RleList` that you can use. I don't have a long `RleList` in hand to test it on…
Answer: Custom CDF creation for HTA 2.0 array using GTF annotation
by
James W. MacDonald
68k
It doesn't appear that Manhong Dai is working at UM any longer, and the webpage appears to have fallen into disrepair (for example, the lin…
Comment: how to use `arrayWeightsQuick()`?
by
matthew
• 0
In the specific use-case I have in mind, `expression` is a simple `matrix` of log2 gene expression per sample, no missing values.
Votes
Answer: BiocParallel_1.40.1.tar.gz not available
Modelling gene program dynamics across time with {lemur}
A: DESeq2 one group vs multiple groups comparison in presence of batch effect
Comment: BiocParallel_1.40.1.tar.gz not available
Comment: BiocParallel_1.40.1.tar.gz not available
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