Showing : bedtools • reset
5
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9
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11k
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subsetByOverlaps : comparing GRANGES and keeping all the information in the METACOLUMNS
granges bedtools intersect
updated 6.3 years ago by ▴ 70 • written 6.3 years ago by ▴ 670
2
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3
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3.0k
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Counting reads in fixed width peaks with DiffBind::dba.count without re-centering?
diffbind chipseq counts peaks bedtools
updated 3.6 years ago by ★ 5.2k • written 6.7 years ago by ▴ 10
0
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0
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1.1k
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I need to measure distance of PAR-CLIP data to RNA regions
parclip bedtools bed files gff3
6.9 years ago linuxborg2 • 0
1
vote
1
reply
1.9k
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Filtering a BED file according to genomic annotation
bed files bedtools filtering chipseq
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 60
0
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4
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1.6k
views
Error: HelloRanges eval
HelloRanges bedtools
7.6 years ago bioinf ▴ 10
2
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7
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2.5k
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Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools
8.8 years ago tmartinez • 0
6 results • Page 1 of 1
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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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