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questions
0
votes
0
replies
783
views
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
Dario Strbenac
★ 1.5k • written 4.8 years ago by
Jurat Shahidin
▴ 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
Martin Morgan
25k • written 7.3 years ago by
Jurat Shahidin
▴ 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
Michael Lawrence
★ 11k • written 7.5 years ago by
Jurat Shahidin
▴ 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
Mike Smith
★ 6.5k • written 7.5 years ago by
Jurat Shahidin
▴ 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
Michael Lawrence
★ 11k • written 7.5 years ago by
Jurat Shahidin
▴ 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
Martin Morgan
25k • written 7.6 years ago by
Jurat Shahidin
▴ 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
Gordon Smyth
50k • written 7.8 years ago by
Jurat Shahidin
▴ 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
Martin Morgan
25k • written 8.2 years ago by
Jurat Shahidin
▴ 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
Michael Lawrence
★ 11k • written 8.1 years ago by
Jurat Shahidin
▴ 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
Hervé Pagès
16k • written 8.2 years ago by
Jurat Shahidin
▴ 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
Hervé Pagès
16k • written 8.2 years ago by
Jurat Shahidin
▴ 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
jon.klonowski
▴ 40 • written 8.2 years ago by
Jurat Shahidin
▴ 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
Hervé Pagès
16k • written 8.3 years ago by
Jurat Shahidin
▴ 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
cherokee1456
• 0 • written 8.3 years ago by
Jurat Shahidin
▴ 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
montuorikandi1759
• 0 • written 8.3 years ago by
Jurat Shahidin
▴ 80
35 results • Page
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