Bioconductor BigWig

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2.6k

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DESeq2 edgeR bigwig limma

3.3 years ago • updated 3.0 years ago Bogdan ▴ 670

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2.9k

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bedgraph wiggleplotr bigwig wig

updated 3.4 years ago by complaintguide • 0 • written 3.4 years ago by Bogdan ▴ 670

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2.2k

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bigWig RNASeqData

4.0 years ago bas_work ▴ 30

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2.8k

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software error BigWig import windows

5.8 years ago lsilva.m • 0

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2.8k

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wiggleplotr bigwig coverage ngs

updated 8.3 years ago by kaur.alasoo ▴ 30 • written 8.3 years ago by borgmichael • 0

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4.3k

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bigwig rtracklayer import granges grangeslist

updated 8.5 years ago by Michael Lawrence ★ 11k • written 8.5 years ago by Assa Yeroslaviz ★ 1.5k

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1.6k

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rtracklayer bigwig import

updated 9.2 years ago by Michael Lawrence ★ 11k • written 9.2 years ago by zx8754 ▴ 10

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1.9k

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bigwig rtracklayer export.bw

updated 9.2 years ago by Michael Lawrence ★ 11k • written 9.2 years ago by story.benjamin ▴ 20

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3.2k

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rtracklayer bigwig

updated 10.0 years ago by laurent.lacroix ▴ 30 • written 10.0 years ago by koneill ▴ 30

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1.6k

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rtracklayer BigWig

updated 10.2 years ago by Michael Lawrence ★ 11k • written 10.2 years ago by dborgesrmit • 0

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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k

Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0

I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…

Comment: Upcoming Ensembl API and data access changes - new blog post available by Hugo Gruson • 0

Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…

Comment: Are individual-mouse-based statistics possible in CellChat? by LillianaVolkman99 • 0

thank you very much. https://www.biostars.org/p/9617271/

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k

My apologies, I forgot that `design.group` is not included in the final matrix, because the baseline group effects are already captured by …

Votes

A: DESeq2: Is it possible to convert read counts to expression values via TPM and r

A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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