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pearsoncorrelation
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Human genes correlation to Bacterial genes
correlation
pearsoncorrelation
rna-seq
differential gene expression
updated 4 months ago by
ATpoint
★ 4.0k • written 6.0 years ago by
saad_k6
• 0
0
votes
0
replies
752
views
How to manage self loop in gene coexpression network constructed using Pearson correlation in Cor() function
rna-seq
gcn
desq2
pearsoncorrelation
5.9 years ago
aishu.jp
▴ 30
0
votes
2
replies
1.8k
views
Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
microarray
pearsoncorrelation
coexpression
spearman
updated 7.2 years ago by
James W. MacDonald
65k • written 7.2 years ago by
juls
• 0
2
votes
1
reply
1.5k
views
DiffBind affinity vs occupancy Heatmaps
diffbind
heatmap
pearsoncorrelation
updated 7.8 years ago by
Rory Stark
★ 5.2k • written 7.8 years ago by
shubhibartaria
▴ 10
4
votes
12
replies
4.7k
views
remove batch effect using limma
limma
rnaseq
batch effect
pearsoncorrelation
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
elpsakkas
• 0
1
vote
2
replies
10k
views
Use of various distance measures and clustering methods in heatmap creation
gplots
heatmap.2
bioconductor
pearsoncorrelation
average
8.8 years ago
svlachavas
▴ 830
6 results • Page
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Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
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…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
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?
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