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1
vote
2
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155
views
Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
10 days ago • updated 9 days ago
ATpoint
★ 4.1k
2
votes
7
replies
1.9k
views
optimHess problem in apeglm/DESeq2
DESeq2
apeglm
updated 11 months ago by
Michael Love
41k • written 12 months ago by
ATpoint
★ 4.1k
2
votes
1
reply
640
views
limma: R-squared for time-series data
limma
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
ATpoint
★ 4.1k
1
vote
2
replies
870
views
biomaRt connection error
biomaRt
updated 2.5 years ago by
Mike Smith
★ 6.5k • written 2.5 years ago by
ATpoint
★ 4.1k
2
votes
1
reply
1.1k
views
apeglm -- influence of reference level on logFC and svalues
DESeq2
apeglm
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
ATpoint
★ 4.1k
4
votes
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 3.5 years ago by
ATpoint
★ 4.1k
0
votes
2
replies
1.3k
views
edgeR for single-cell data with inferential replicates
edgeR
alevin
3.6 years ago
ATpoint
★ 4.1k
2
votes
1
reply
1.2k
views
normOffsets in csaw
csaw
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
ATpoint
★ 4.1k
2
votes
3
replies
1.1k
views
vst with output of edgeR::calcNormFactors
DESeq2
updated 18 months ago by
Gordon Smyth
50k • written 3.7 years ago by
ATpoint
★ 4.1k
3
votes
3
replies
2.4k
views
Cell cycle regression for scRNA-seq data
OSCA
batchelor
cell cycle regression
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
ATpoint
★ 4.1k
2
votes
1
reply
1.1k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
ATpoint
★ 4.1k
3
votes
1
reply
1.0k
views
Output lfc for Wilcox-based findMarkers
scran
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
ATpoint
★ 4.1k
6
votes
11
replies
2.1k
views
Correct use of tximport in combination with edgeR cpm()
tximport
edgeR
5.0 years ago • updated 4.3 years ago
ATpoint
★ 4.1k
2
votes
1
reply
947
views
Using Input Samples in ChIP-seq Differential Analysis (csaw/edgeR)
csaw
chip-seq
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
ATpoint
★ 4.1k
0
votes
0
replies
1.1k
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools
rtracklayer
4.5 years ago • updated 4.4 years ago
ATpoint
★ 4.1k
3
votes
1
reply
1.6k
views
Correct use of TMM / normalization factors based on large bins
csaw
TMM
4.7 years ago
ATpoint
★ 4.1k
2
votes
2
replies
702
views
InTAD: Sample Size and Statistical Power
InTAD
updated 4.8 years ago by
Konstantin Okonechnikov
▴ 40 • written 4.8 years ago by
ATpoint
★ 4.1k
2
votes
1
reply
972
views
Deactivate svalue=T in lfcShrink - DESeq2 - apeglm
deseq2
apeglm
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
ATpoint
★ 4.1k
4
votes
4
replies
2.1k
views
Unexpected MAplot after apeglm shrinkage in DESeq2
apeglm
deseq2
rna-seq
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
ATpoint
★ 4.1k
2
votes
1
reply
997
views
Significant reporter activity with mpralm function
mpra
mpralm
reporter assay
linear model
5.9 years ago
ATpoint
★ 4.1k
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