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R
•
reset
2
votes
27
replies
4.0k
views
CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for regions < 200kb
crisprseek
sgrna
crispr
cas9
R
8.6 years ago • updated 8.5 years ago
alexgraehl
▴ 20
2
votes
13
replies
3.1k
views
problems filtering antigenomic probes from HTA 2.0
pd.hta.2.0
R
7.7 years ago • updated 7.2 years ago
s.munster
▴ 40
0
votes
5
replies
1.7k
views
xps package - import.expr.scheme help
xps
root
R
affy
updated 7.3 years ago by
cstrato
★ 3.9k • written 7.3 years ago by
jordansquair
• 0
0
votes
15
replies
2.5k
views
Is the STRINGdb server down?
STRINGdb
R
protein
updated 4.9 years ago by
zhanghongjie000
• 0 • written 5.1 years ago by
shahroze786
• 0
2
votes
7
replies
1.4k
views
modifying compound datasets
R
6.3 years ago
harbydonald
• 0
1
vote
22
replies
4.7k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor
R
annotationforge
updated 7.3 years ago by
theobroma22
▴ 10 • written 7.8 years ago by
wssdandan2009
• 0
3
votes
5
replies
2.0k
views
CRAN policy and Bioconductor policy
r
cran
updated 9.4 years ago by
Henrik Bengtsson
★ 2.4k • written 9.4 years ago by
mattocci27
• 0
0
votes
7
replies
1.8k
views
DESeq2 with interest only for 1 gene
R
deseq2
differential gene expression
help
7.9 years ago
fischer87
• 0
1
vote
19
replies
25k
views
Import bamfiles for RNAsequencing analysis
R
rnaseq
bam file
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
Merlin
▴ 10
6
votes
10
replies
4.8k
views
defining a function for multiple paired t.test in many rows of a microarray dataset
microarray
r
t.test
bioconductor
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
svlachavas
▴ 830
7
votes
13
replies
2.2k
views
Test whether expression levels of two gene sets are significantly different
R
DESeq2
gene set testing
gene expression
7.5 years ago
Jon Bråte
▴ 250
8
votes
11
replies
1.9k
views
Creating design matrix in LIMMA
limma
microarray
R
7.3 years ago
sgblackpearl
• 0
1
vote
3
replies
2.4k
views
getSequence from biomaRt but Error in martCheck
R
biomart
ensemble mart
updated 8.5 years ago by
Hervé Pagès
16k • written 8.5 years ago by
Gabriela Santos
• 0
8
votes
9
replies
6.0k
views
could not find symbol "keepNA" in environment of the generic function
R
function
genomicalignments
genomicranges
summarizeoverlaps
updated 8.8 years ago by
Mathilde
• 0 • written 8.8 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
3
replies
1.4k
views
Our mart (on https) is not compatible with biomaRt access. What's wrong?
R
biomart
biomaRt
updated 8.0 years ago by
biomartdev
▴ 10 • written 8.0 years ago by
JWCarlson
▴ 80
4
votes
3
replies
4.6k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq
rsubread
featurecounts
r
9.5 years ago
gustavoborin01
• 0
0
votes
3
replies
1.6k
views
problem with oneChannelGUI
onechannelgui
exon array analysis
R
8.5 years ago
anna.dolnik
• 0
5
votes
22
replies
5.5k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor
annotationforge
annotationdbi
annotation
r
updated 7.8 years ago by
Axel Klenk
★ 1.0k • written 9.2 years ago by
Stephen H
• 0
0
votes
3
replies
1.4k
views
Error in frameCounting using riboSeqR
riboseq
R
riboseqr
6.7 years ago
yingyingguo0228
• 0
0
votes
3
replies
2.0k
views
Change order of conditions when plotting: plotCounts {DESeq2}
R
deseq2
plotcounts
5.0 years ago
ecg1g15
▴ 20
1
vote
3
replies
3.0k
views
Reactome pathway analysis using ReactomePA
reactomepa
R
bioconductor
ReactomePA
updated 8.6 years ago by
kmezhoud
▴ 10 • written 8.6 years ago by
Deepak Tanwar
▴ 10
0
votes
6
replies
1.8k
views
Manipulating random CRISPR sequences
r
crispr
updated 7.9 years ago by
mousheng xu
▴ 10 • written 8.5 years ago by
shane
• 0
3
votes
3
replies
1.8k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps
R
bioconductor
rnaseq
rna-seq
updated 7.2 years ago by
Hervé Pagès
16k • written 7.2 years ago by
Walter F. Baumann
▴ 10
0
votes
3
replies
2.5k
views
warning: example doesn't exist; while trying to build a package
bioconductor
package development
R
roxygen2
warning
6.5 years ago
clarisbaby
• 0
10
votes
13
replies
4.3k
views
Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
R
limma
oligo
differential gene expression
affymetrix microarrays
updated 8.8 years ago by
tree-ski
• 0 • written 8.8 years ago by
dennis.oezcelik
▴ 10
0
votes
3
replies
2.3k
views
Problem with sbml packages
R
8.9 years ago
fabien.chambodut
• 0
1
vote
5
replies
1.6k
views
Making package compatible with old version of R/Bioconductor
bioconductor
R
software error
biocinstaller
7.9 years ago
gabriel.hoffman
▴ 110
2
votes
4
replies
2.1k
views
running msa (msa) aborts R session
msa
alignment
r
software error
written 6.4 years ago by
ans74
• 0
4
votes
4
replies
2.6k
views
Non-specific filtering methodogies for ExpressionSet in R/Bioconductor
genefilter
R
bioconductor
differential gene expression
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
svlachavas
▴ 830
0
votes
5
replies
1.6k
views
MEDIPS genome Vs createROIset significance issue
medips
r
8.2 years ago
peter.mcerlean
• 0
2
votes
10
replies
20k
views
Heatmap with error message: `x' must be a numeric matrix
r
heatmap
numericmatrix
updated 8.1 years ago by
Assa Yeroslaviz
★ 1.5k • written 8.1 years ago by
Biologist
▴ 110
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 2.4 years ago by
jon.klonowski
▴ 40 • written 8.3 years ago by
Jurat Shahidin
▴ 80
0
votes
5
replies
5.5k
views
Blastp - through R
blast
R
8.2 years ago
maahpishanu
• 0
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
0
votes
4
replies
1.6k
views
IONiseR readFast5Summary Error
R
sequencing
preprocessing
bioconductor
updated 8.4 years ago by
Mike Smith
★ 6.5k • written 8.4 years ago by
mariandhore
• 0
3
votes
4
replies
1.8k
views
Network generation from adjacency matrix of zeroes and ones
R
adjacency matrix
mirna
8.4 years ago
alptaciroglu
▴ 50
2
votes
9
replies
20k
views
Error in file(con, “r”) : cannot open the connection
r
phyloseq
import_biom
otu
qiime
updated 8.6 years ago by
mcmurdie
▴ 20 • written 8.6 years ago by
moanam
• 0
6
votes
2
replies
1.8k
views
permutation test against intervals
R
pkg
updated 8.9 years ago by
bgel
▴ 30 • written 9.1 years ago by
csc.csclogin.login40
▴ 20
4
votes
8
replies
7.0k
views
getGEO - cannot Open URL issue
getGEO
R
GEOquery
8.6 years ago
alptaciroglu
▴ 50
3
votes
5
replies
7.3k
views
WGCNA HELP - Error: REAL() can only be applied to a 'numeric', not a 'integer'
wgcna
rnaseq
R
bioconductor
updated 8.3 years ago by
Peter Langfelder
★ 3.0k • written 8.3 years ago by
sm15766
▴ 30
0
votes
5
replies
2.2k
views
Question about the database version and MAF value in biomaRt
R
biomart
MAF
updated 8.7 years ago by
Thomas Maurel
▴ 800 • written 8.7 years ago by
jz6002
• 0
1
vote
3
replies
1.0k
views
Regular Expressions language R
regular expressions R
R
regular expressions
updated 8.8 years ago by
Martin Morgan
25k • written 8.8 years ago by
fabien.chambodut
• 0
6
votes
3
replies
7.0k
views
Heatmap Plotting in R
heatmap
R
bioconductor
8.8 years ago • updated 7.1 years ago
Deepak Tanwar
▴ 10
0
votes
3
replies
1.4k
views
Default Rapidr invalid class “SummarizedExperiment”
software error
RAPIDR
summarizeoverlaps
R
8.6 years ago
Pau Marc Muñoz Torres
▴ 20
0
votes
3
replies
1.6k
views
Function for barplot
R
9.5 years ago
dktarathym
• 0
1
vote
2
replies
2.1k
views
how to perform pre ranked GSEA in R?
r
microarray
statistics
GSEA
updated 7.2 years ago by
predeus
• 0 • written 9.2 years ago by
Nemo
▴ 80
0
votes
2
replies
1.4k
views
get LCMS masses with more significant figures with xcmsRaw()
R
xcms
xcmsRaw
LC
updated 8.8 years ago by
Johannes Rainer
★ 2.0k • written 8.8 years ago by
phoenix
• 0
2
votes
7
replies
1.6k
views
To build SVM model for amino acid using composition of AA in r.
svm
r
8.8 years ago
pujapatel5400
• 0
1
vote
5
replies
2.1k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.2 years ago by
chandlerjd58
▴ 10
2
votes
2
replies
6.7k
views
R 3.2.0 problem with DESeq2 - Hmisc error
deseq2
r
software error
updated 9.0 years ago by
Steve Lianoglou
★ 13k • written 9.0 years ago by
rclaire
▴ 20
50 results • Page
1 of 1
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Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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