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0
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Any recommended workflow for incrementally selecting top ranked genes by using mRMR feature selection?
microarray gene-filtering mRMR parallel-processing bioconductor-package
4.7 years ago Jurat Shahidin ▴ 80
2
votes
3
replies
983
views
How can I overcome the error of "No residual degrees of freedom in linear model fits"?
limma microarray error
updated 4.8 years ago by ★ 1.5k • written 4.8 years ago by ▴ 80
9
votes
10
replies
2.1k
views
Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
limma microarray genefilter deseq2
4.8 years ago Jurat Shahidin ▴ 80
6
votes
8
replies
1.7k
views
How to find out the genes that changes in expression by using gene level expression data matrix?
limma microarray affy edger
4.8 years ago Jurat Shahidin ▴ 80
2
votes
4
replies
1.7k
views
How to render summary list for `GRangesList` by using `SummarizedExperiment` package?
r summarizedexperiment grangeslist
7.1 years ago Jurat Shahidin ▴ 80
1
vote
4
replies
5.0k
views
do.call error "second argument must be a list" with GRanges object [closed]
r error handling
7.2 years ago Jurat Shahidin ▴ 80
3
votes
16
replies
4.1k
views
Any way to proceed duplicate removal for list of GRanges object ?
r grangeslist duplicate
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 80
0
votes
5
replies
1.4k
views
How to plot benchmark result of R/ Bioconductor package (getting curve or line graph)?
r benchmark performance ggplot2
7.3 years ago Jurat Shahidin ▴ 80
1
vote
3
replies
1.4k
views
Any way to debug unusual vignette error when building package?
r compilation error error handling data.table
7.3 years ago Jurat Shahidin ▴ 80
0
votes
2
replies
1.5k
views
How to take sample peak from each chromosome in peak bed files ?
r chipseq encode peak
7.4 years ago Jurat Shahidin ▴ 80
5
votes
2
replies
1.4k
views
seeking idea for proper output representation for multiple GRanges overlapping
r grangeslist biocparallel findoverlaps
7.8 years ago • updated 7.4 years ago Jurat Shahidin ▴ 80
5
votes
3
replies
1.3k
views
How to avoid repeated overlap pair for GRanges object in grid?
r genomicranges
7.7 years ago • updated 7.4 years ago Jurat Shahidin ▴ 80
2
votes
2
replies
972
views
Any way to speed up splitting relatively big GRanges objects by given threshold ?
r granges split performance
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ▴ 80
3
votes
5
replies
17k
views
Any quick solution for fixing error : "$ operator is invalid for atomic vectors" ?
r granges dplyr error handling
updated 7.5 years ago by ★ 6.5k • written 7.5 years ago by ▴ 80
2
votes
4
replies
1.2k
views
How to remove duplicated overlap hit index in IntegerList efficiently [solved] ?
r iranges integerlist
7.5 years ago Jurat Shahidin ▴ 80
2
votes
4
replies
1.5k
views
Any way to combine two GRangesList easily ?
genomicranges grangeslist r
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ▴ 80
3
votes
4
replies
1.3k
views
Any way to detach or simplify nested GRangesList ?
grangeslist filtering r
7.6 years ago Jurat Shahidin ▴ 80
2
votes
1
reply
943
views
Few doubt about new package submission
bioconductor submit package
updated 7.6 years ago by 25k • written 7.6 years ago by ▴ 80
2
votes
2
replies
1.1k
views
How to detect and replace zero index in IntegerList ?
iranges integerlist s4
7.7 years ago Jurat Shahidin ▴ 80
3
votes
5
replies
1.3k
views
How to sort set of GRanges object in the list by increasing order?
granges grangeslist genomicranges
7.7 years ago Jurat Shahidin ▴ 80
4
votes
2
replies
1.2k
views
seeking a paper or journal review about repeated multiple testing for Biological ChIP-seq replicates?
bioinformatics paper multiple treatments biologicalreplicates
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 80
2
votes
2
replies
1.2k
views
getting global Fisher score for overlap of 3 GRanges object by element-wise [solved]
r DataFrame fisher-method
7.8 years ago Jurat Shahidin ▴ 80
3
votes
5
replies
1.7k
views
How can I coerce "list" to S4 "List" (reproducible example is available)?
coercion data manipulation s4vectors List
7.8 years ago Jurat Shahidin ▴ 80
28
votes
43
replies
8.4k
views
Find overlap for more than 2 GRanges object simultaneously (reproducible example is updated) ?
findoverlaps granges
updated 8.0 years ago by 25k • written 8.2 years ago by ▴ 80
9
votes
6
replies
2.8k
views
Any method can coerce "list" object to GRanges [reproducible example is included]?
granges error handling R
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ▴ 80
3
votes
6
replies
1.1k
views
How to replace NAs values in "CompressedIntegerList" objects [reproducible example is included] ?
r bug granges
8.1 years ago Jurat Shahidin ▴ 80
0
votes
4
replies
3.3k
views
[Solved]Preserve metadata column for retrieving common regions from two GRanges objects
granges intersect
8.1 years ago Jurat Shahidin ▴ 80
6
votes
7
replies
4.1k
views
unexpected error when creating GRanges object by calling makeGRangesFromDataFrame()
r error handling granges
updated 8.2 years ago by 16k • written 8.2 years ago by ▴ 80
7
votes
6
replies
2.0k
views
Help to find Volunteer who can review my bioconductor package before submission ?
r packages submission
8.2 years ago Jurat Shahidin ▴ 80
3
votes
2
replies
1.3k
views
What is the main difference between nclist and intervaltree algorithm in GenomicRanges packages ?
nclist genomeintervals
updated 8.2 years ago by 16k • written 8.2 years ago by ▴ 80
1
vote
4
replies
10k
views
Couldn't install GenomicRanges packages after update bioconductor to 3.2 version ?
bioconductor error handling
8.2 years ago Jurat Shahidin ▴ 80
6
votes
11
replies
7.3k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges split r
updated 2.3 years ago by ▴ 40 • written 8.2 years ago by ▴ 80
6
votes
7
replies
1.8k
views
How to implement element-wise-overlaps with iteration for two different bed files in R?
r findoverlaps iterators
updated 8.3 years ago by 16k • written 8.3 years ago by ▴ 80
3
votes
2
replies
2.1k
views
How to do simple Fisher' exact test for overlapped genomic interval in R?
test fisher exact r findoverlapsofpeaks
updated 12 months ago by • 0 • written 8.3 years ago by ▴ 80
0
votes
3
replies
1.5k
views
How to extract / pull out each row(a.k.a, single genome interval ) from given bed files by row by row for meta analysis?
r bioinformatics peakset
updated 12 months ago by • 0 • written 8.3 years ago by ▴ 80
35 results • Page 1 of 1
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