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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
3.2k
views
problems filtering antigenomic probes from HTA 2.0
pd.hta.2.0
R
7.8 years ago • updated 7.3 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 5.0 years ago by
zhanghongjie000
• 0 • written 5.2 years ago by
shahroze786
• 0
2
votes
7
replies
1.4k
views
modifying compound datasets
R
6.4 years ago
harbydonald
• 0
1
vote
22
replies
4.7k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor
R
annotationforge
updated 7.4 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 9.5 years ago by
Henrik Bengtsson
★ 2.4k • written 9.5 years ago by
mattocci27
• 0
0
votes
7
replies
1.9k
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 6.1 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
2.3k
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
2.0k
views
Creating design matrix in LIMMA
limma
microarray
R
7.4 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 8.9 years ago by
Mathilde
• 0 • written 8.9 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 8.1 years ago by
biomartdev
▴ 10 • written 8.1 years ago by
JWCarlson
▴ 80
4
votes
3
replies
4.7k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq
rsubread
featurecounts
r
9.6 years ago
gustavoborin01
• 0
0
votes
3
replies
1.6k
views
problem with oneChannelGUI
onechannelgui
exon array analysis
R
8.6 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 9.3 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
3.1k
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 8.0 years ago by
mousheng xu
▴ 10 • written 8.6 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
6.6 years ago • updated 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 8.9 years ago by
tree-ski
• 0 • written 8.9 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
8.0 years ago
gabriel.hoffman
▴ 110
2
votes
4
replies
2.1k
views
running msa (msa) aborts R session
msa
alignment
r
software error
written 6.5 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 9.4 years ago by
Gordon Smyth
50k • written 9.4 years ago by
svlachavas
▴ 830
0
votes
5
replies
1.6k
views
MEDIPS genome Vs createROIset significance issue
medips
r
8.3 years ago • updated 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 8.2 years ago by
Assa Yeroslaviz
★ 1.5k • written 8.2 years ago by
Biologist
▴ 110
6
votes
11
replies
7.4k
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
5.6k
views
Blastp - through R
blast
R
8.3 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 8.5 years ago by
mariandhore
• 0
3
votes
4
replies
1.9k
views
Network generation from adjacency matrix of zeroes and ones
R
adjacency matrix
mirna
8.5 years ago • updated 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 9.0 years ago by
bgel
▴ 30 • written 9.2 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
7.4k
views
WGCNA HELP - Error: REAL() can only be applied to a 'numeric', not a 'integer'
wgcna
rnaseq
R
bioconductor
updated 8.4 years ago by
Peter Langfelder
★ 3.0k • written 8.4 years ago by
sm15766
▴ 30
0
votes
5
replies
2.3k
views
Question about the database version and MAF value in biomaRt
R
biomart
MAF
updated 8.8 years ago by
Thomas Maurel
▴ 800 • written 8.8 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
8.7 years ago • updated 8.6 years ago
Pau Marc Muñoz Torres
▴ 20
0
votes
3
replies
1.6k
views
Function for barplot
R
9.6 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 8.9 years ago by
Johannes Rainer
★ 2.0k • written 8.9 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
8.9 years ago
pujapatel5400
• 0
1
vote
5
replies
2.2k
views
pd.mogene.2.0st Error Installing in R 3.1.2
oligo
microarray
r
bioconductor
written 9.3 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 9.1 years ago by
Steve Lianoglou
★ 13k • written 9.1 years ago by
rclaire
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…
Comment: Errors in chromosome annotation-biomaRt
by
blackwidowzzz
• 0
I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …
Answer: Errors in chromosome annotation-biomaRt
by
James W. MacDonald
66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat
by
James W. MacDonald
66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons
by
James W. MacDonald
66k
In that case, probably easiest to subset to the groups being compared.
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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