Showing : time-series • reset
2
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10
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2.8k
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Time-series analysis with DESeq2
deseq2 time-series design matrix edger
updated 5.2 years ago by 41k • written 5.2 years ago by ★ 1.5k
1
vote
6
replies
893
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Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
0
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5
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1.8k
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RNA-seq time course analysis with only one experimental condition
deseq2 cancer rna-seq time-series
4.8 years ago mah19 • 0
1
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5
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1.5k
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Time course DE analysis in DESeq2 with Wald test
DESeq2 time-series
updated 6.5 years ago by 41k • written 6.5 years ago by ▴ 10
1
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4
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1.3k
views
Analysis Time course data using DESeq2
deseq2 timecourse multiple time points time-series
updated 5.8 years ago by 41k • written 5.8 years ago by • 0
0
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3
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1.0k
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time-series, no replicates, no control groupe
deseq2 time-series without replicate
updated 5.8 years ago by 41k • written 5.8 years ago by • 0
0
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2
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779
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R: problem with running time-series analysis software: Mfuzz
time-series mfuzz replace=FALSE
23 months ago soda ▴ 80
0
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1
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610
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Interpreting results from DESeq2 time-series multifactorial data analysis
DESeq2 time-series timecoursedata timecourse multifactorial
updated 17 months ago by 41k • written 18 months ago by • 0
0
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1
reply
815
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DEseq2 to test half-life for time-series data
half-life DESeq2 time-series
updated 3.0 years ago by 41k • written 3.0 years ago by ▴ 10
9 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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