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mlseq
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Data preparation and Machine learning on time course RNAseq data
machine learning
deep learning
RNAseq
MLSeq
5.3 years ago
A
▴ 40
0
votes
0
replies
942
views
MLSeq plot results
MLSeq
7.4 years ago
jonessara770
▴ 10
0
votes
0
replies
1.6k
views
Hierarchical Random Forest classifier
rnaseq
machinelearning
random forest
mlseq
8.2 years ago
anthony.hawkins
▴ 10
0
votes
2
replies
1.2k
views
MLSeq package: using z-score normalized data as input?
MLSeq
8.5 years ago
philipp24
▴ 30
0
votes
3
replies
1.5k
views
MLSeq Mathematical Concepts
Classification
edgeR
DESeq
MLSeq
Classification
edgeR
DESeq
MLSeq
updated 10.0 years ago by
Wolfgang Huber
★ 13k • written 10.0 years ago by
Dario Strbenac
★ 1.5k
5 results • Page
1 of 1
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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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