Showing : RNAseq • reset
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 1 day ago by 41k • written 1 day ago by • 0
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 3 days ago by 50k • written 3 days ago by • 0
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
6 days ago • updated 4 days ago catv • 0
3
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1
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Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 8 days ago by • 0
0
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1
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 7 days ago by 41k • written 8 days ago by • 0
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122
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 16 days ago by ★ 4.0k • written 17 days ago by • 0
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 2 days ago by ★ 1.2k • written 13 months ago by ▴ 10
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 8 days ago by • 0 • written 17 months ago by • 0
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biomart not ound some prevous release
biomart rnaseq
written 5.2 years ago by ▴ 40
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1.8k
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EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 24 days ago by 50k • written 11.5 years ago by ▴ 30
10 results • Page 1 of 1
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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona • 0
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
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'…
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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