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Restricting differential binding analysis to only TSS-proximal regions
ChIP
csaw
updated 11 days ago by
Aaron Lun
★ 28k • written 12 days ago by
Luca
• 0
0
votes
1
reply
1.6k
views
use diffbind with normilized bedgraph files from spike ins
diffbind
chip-seq
chip
spike
spike-ins
updated 4.7 years ago by
Rory Stark
★ 5.2k • written 4.8 years ago by
Theo
▴ 10
5
votes
7
replies
2.7k
views
ChIPSeeker enrichPeakOverlap external dataset downloads
chipseeker
chipseq
chip
updated 7.1 years ago by
Guangchuang Yu
★ 1.2k • written 7.1 years ago by
rbronste
▴ 60
1
vote
5
replies
1.8k
views
Coerce several Granges objects to a GrangeList
GRanges
GRangesList
ChIP
10.4 years ago
patrick.schordert
▴ 30
4 results • Page
1 of 1
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Comment: GSVA on RNAseq data
by
Bob
▴ 10
Hi Robert, We were actually very interested in this problem in particular. It seems that using counts for gene sets with varying gene leng…
Comment: plyranges: find exact GRanges match keeping metadata columns
by
Michael Love
43k
But I will say if you are doing a lot of these, and require exact match, just making it a simple key -- eg `paste0(start,".",end)` -- seems…
Answer: Comparing Mock vs Infected in WT and Knockout Cells
by
Michael Love
43k
I recommend for questions about statistical analysis plan to meet with a local statistician or someone familiar with linear models in R. I …
Answer: In WGCNA, what networkType should be used in pickSoftThreshold for a Signed Nowi
by
ATpoint
★ 4.6k
WGCNA is no Bioconductor package. Consider biostars.org or bioinformatics Reddit, but if you do show a bit more effort please. People appre…
Answer: Error: lexical error: invalid char in json text (alevin-seurat)
by
ATpoint
★ 4.6k
Two things: 1) See https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#Alevin -- Your `colon_file`…
Votes
A: how to extract Granges not overlapping with other ganges?
DESeq2 1.20.0 lfcshrink function
A: LIMMA on RT-PCR data
Answer: Efficiently working with HDF5-backed SingleCellExperiments
Efficiently working with HDF5-backed SingleCellExperiments
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Vincent J. Carey, Jr.
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