Biostar Htseqtools

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203

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Deprecation chipseq htseqtools Bioconductor

updated 4 months ago by Basti ▴ 150 • written 4 months ago by Mick • 0

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1.8k

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htseqtools deseq2 counts cuffdiff

5.5 years ago Jon Bråte ▴ 180

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928

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Coverage htSeqTools Coverage htSeqTools

updated 9.5 years ago by Valerie Obenchain ★ 6.7k • written 9.5 years ago by Juan L. Mateo ▴ 80

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1.2k

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GenomicRanges htSeqTools GenomicRanges htSeqTools

updated 9.5 years ago by Vincent J. Carey, Jr. 6.5k • written 9.5 years ago by Juan L. Mateo ▴ 80

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501

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IRanges htSeqTools IRanges htSeqTools

updated 9.5 years ago by Michael Lawrence 11k • written 9.5 years ago by Ian Donaldson ▴ 70

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509

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convert htSeqTools convert htSeqTools

9.5 years ago Oscar Reina ▴ 20

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683

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htSeqTools ASSIGN htSeqTools ASSIGN

updated 9.5 years ago by Michael Lawrence 11k • written 9.5 years ago by Ian Donaldson ▴ 70

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Answer: Wrong stdev.unscaled from contrasts.fit when lmFit contains a weights matrix by Gordon Smyth 43k

First, the design matrix and contrast you have created are extremely artificial and I cannot see how they could be used for any real analys…

Answer: Help With TCGAbiolinks package by Kevin Blighe 3.2k

Hi Daniela, The raw counts should be contained in the `HGNC.exp` object under the '`raw_count`' assay: HNSC.exp class: RangedSum…

Comment: Problems with installation of 'phyloseq by Kevin Blighe 3.2k

Great, thanks for the feedback, Ina

Comment: featureCounts - paired-end data by Wei Shi ★ 3.3k

You need to specify `-p` and `--countReadPairs` to count fragments instead of reads. The value provided to the `-t` option is typically `ex…

Comment: Problems with installation of 'phyloseq by Ina • 0

Hello, I used the code to install 'GenomeInfoDbData' from Bioconductor- which worked. Then I tried to install 'phyloseq' from Bioconductor…

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Answer: Apparent Ensembl - Entrez gene mis-match in org.Mm.eg.db.

Answer: Macbook M1 install genefilter failed

Comment: derfinder model.matrix with limma or single base-level F-statistics analysis

Answer: derfinder model.matrix with limma or single base-level F-statistics analysis

A: DESeq2: multiple conditions design -- How to select subset comparisons from the

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