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GenomicFiles
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Error in fragEnds[, 1] : incorrect number of dimensions while using printWigFile function in Basic4Cseq package
GenomicInteractions
Basic4Cseq
DNASeq
GenomicFiles
2.8 years ago
koushik
• 0
2
votes
6
replies
1.2k
views
memory leak when subsampling BAM
GenomicFiles
ShortRead
Rsamtools
3.2 years ago
robmaz77
▴ 20
1
vote
2
replies
734
views
The metadata from rowRanges is missing in the MAP function of GenomicFiles.
GenomicFiles
updated 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
Qiang
▴ 80
3
votes
2
replies
955
views
ranges input for GenomicFiles
genomicfiles
updated 6.3 years ago by
Martin Morgan
25k • written 6.3 years ago by
Qiang
▴ 80
3
votes
2
replies
1.1k
views
Passing multiple arguments (like mapply) to the MAP-function in GenomicFiles.
genomicfiles
reduceByRange
updated 6.6 years ago by
Valerie Obenchain
★ 6.8k • written 6.6 years ago by
maltethodberg
▴ 170
3
votes
3
replies
1.1k
views
Parallel reading of Vcfs using VcfStack/RangedVcfStack
GenomicFiles
BiocParallel
updated 6.8 years ago by
shepherl
3.8k • written 6.9 years ago by
m.van_iterson
▴ 20
4
votes
2
replies
1.3k
views
readGAlignmentPairs not working correctly when reading a bam file by chunks
rsamtools
genomicalignments
genomicfiles
updated 7.8 years ago by
Hervé Pagès
16k • written 7.8 years ago by
jfiksel
▴ 30
1
vote
1
reply
1.4k
views
How to randomly sample bam files obtaining a subset of information (ex: binning locations)
genomicfiles
rsamtools
updated 7.8 years ago by
Martin Morgan
25k • written 7.8 years ago by
victoriaccorey
▴ 10
2
votes
2
replies
2.5k
views
How to randomly sample BAM files
rsamtools
genomicalignments
genomicfiles
updated 8.7 years ago by
Martin Morgan
25k • written 8.7 years ago by
Welliton de Souza
▴ 70
0
votes
0
replies
972
views
[Bioc-devel] AnnotatioDbi Biostrings load order breaks GenomicFiles summary method
GO
Biostrings
rtracklayer
GenomicRanges
BiocParallel
GenomicFiles
9.6 years ago
Dan Tenenbaum
★ 8.2k
10 results • Page
1 of 1
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Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs
by
sredemption
• 0
Try library(enrichplot) dotplot(gsea_FS, showCategory=10, split=".sign") + facet_grid(.~.sign)
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you for your reply and I know there is another post similar to this you had mentioned this. How are the genes that I mentioned in the…
Answer: FGSEA pre-ranked input in increasing order or decreasing
by
alserg
▴ 240
The genes are automatically ordered within `fgsea`, there is no need to sort them manually.
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
ATpoint
★ 4.0k
Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.
Comment: significant difference of p-values with dream() after updating VariancePartition
by
gabriel.hoffman
▴ 100
See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…
Votes
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
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W. Evan Johnson
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Alejandro Reyes
★ 1.9k
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shepherl
3.8k
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