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Convert
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0
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21
replies
3.2k
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How to annotate genomic coordinates
convert
convert
11.5 years ago
José Luis Lavín
▴ 280
0
votes
21
replies
6.6k
views
BAM files to Genomic Ranges object
Alignment
convert
Repitools
Alignment
convert
Repitools
updated 5 months ago by
Marge
• 0 • written 11.3 years ago by
José Luis Lavín
▴ 280
0
votes
13
replies
1.3k
views
rtracklayer GraphTrackLine
convert
convert
updated 14.0 years ago by
Michael Lawrence
★ 11k • written 14.0 years ago by
Dario Strbenac
★ 1.5k
0
votes
13
replies
2.2k
views
CHARM - The following columns in sampleKey...
convert
charm
convert
charm
updated 11.5 years ago by
Andrew Jaffe
▴ 120 • written 11.5 years ago by
Guest User
★ 13k
0
votes
12
replies
2.7k
views
BioMart and Ensembl questions
convert
biomaRt
convert
biomaRt
updated 14.6 years ago by
Paul Leo
▴ 970 • written 14.7 years ago by
jiayu wen
▴ 10
0
votes
11
replies
4.1k
views
creating GRanges and reading BAM files
Coverage
convert
Coverage
convert
updated 12.2 years ago by
Sunny Yu Liu
▴ 80 • written 12.2 years ago by
David A.
▴ 70
0
votes
10
replies
1.8k
views
How to convert from IRanges(List) to Rle(List)
convert
IRanges
convert
IRanges
updated 12.1 years ago by
Martin Morgan
25k • written 12.1 years ago by
delhomme@embl.de
★ 1.2k
0
votes
10
replies
2.2k
views
MethyLumiM to MethyLumiSet?
convert
lumi
methylumi
minfi
wateRmelon
convert
lumi
methylumi
minfi
wateRmelon
updated 10.5 years ago by
Tim Triche
★ 4.2k • written 10.5 years ago by
Martin Rijlaarsdam
▴ 190
0
votes
10
replies
1.6k
views
biomaRt manual
affy
convert
biomaRt
affy
convert
biomaRt
updated 17.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 17.1 years ago by
Weiwei Shi
★ 1.2k
0
votes
9
replies
2.6k
views
ReportingTools gene IDs
convert
convert
updated 10.0 years ago by
James W. MacDonald
65k • written 10.0 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
9
replies
1.8k
views
EBImage Error in .Call("lib_readImages", as.character(files), as.integer(colormode),
convert
convert
updated 13.1 years ago by
Gregoire Pau
▴ 310 • written 13.1 years ago by
Vladimir Morozov
▴ 130
0
votes
8
replies
1.9k
views
Converting list to a matrix
convert
convert
updated 13.1 years ago by
Arunava Chakravartty
▴ 50 • written 13.1 years ago by
pankaj borah
▴ 120
0
votes
8
replies
1.4k
views
HuGene annotation and htmls
Annotation
convert
xps
Annotation
convert
xps
updated 15.1 years ago by
Marc Carlson
★ 7.2k • written 15.1 years ago by
Mayte Suarez-Farinas
▴ 510
0
votes
8
replies
3.2k
views
Reading Agilent files using read.maimages
Survival
DynDoc
genefilter
tkWidgets
affy
vsn
marray
convert
ArrayExpress
Survival
affy
updated 16.7 years ago by
Scott Reagan Franklin
▴ 20 • written 16.7 years ago by
Steve Taylor
▴ 100
0
votes
8
replies
3.6k
views
DESeq and transcript-wise analysis
convert
DESeq
convert
DESeq
12.2 years ago
Elena Sorokin
▴ 150
0
votes
8
replies
2.2k
views
methyAnalysis for DMR identification
convert
methyAnalysis
convert
methyAnalysis
updated 10.2 years ago by
Giovanni Calice
▴ 160 • written 10.2 years ago by
Guest User
★ 13k
0
votes
8
replies
1.6k
views
CRytoscape: an early release
convert
convert
updated 13.8 years ago by
J.delasHeras@ed.ac.uk
★ 1.9k • written 13.8 years ago by
Paul Shannon
★ 1.1k
0
votes
7
replies
1.7k
views
Approaches to building Rle sequences from ranges
GO
convert
GO
convert
updated 9.9 years ago by
Jeff Johnston
▴ 90 • written 9.9 years ago by
Vince S. Buffalo
▴ 40
0
votes
7
replies
2.2k
views
methyAnalysis error
GO
convert
methylumi
genoset
GO
convert
methylumi
genoset
10.5 years ago
Juan Fernández Tajes
▴ 190
0
votes
7
replies
1.3k
views
Limma question_Intra-Spot Correlation Question
Normalization
limma
PROcess
convert
Normalization
limma
PROcess
convert
updated 12.2 years ago by
Gordon Smyth
50k • written 12.3 years ago by
jgomez@uni-potsdam.de
▴ 30
0
votes
7
replies
1.6k
views
converting Affy indices to x,y coordinates
cdf
probe
convert
cdf
probe
convert
updated 13.2 years ago by
Mounts, William
▴ 30 • written 13.2 years ago by
Todd Allen
▴ 20
1
vote
7
replies
2.2k
views
Can XCMS output continuum/profile data to netCDF format?
xcms
convert
protein
updated 7.4 years ago by
Johannes Rainer
★ 2.0k • written 7.4 years ago by
ray.bacala
• 0
0
votes
6
replies
2.6k
views
converting position from '-' strand to '+' strand
convert
convert
updated 22 months ago by
analeonpalacio
▴ 10 • written 14.1 years ago by
Tim Smith
★ 1.1k
0
votes
6
replies
1.5k
views
Is there a package or a way to convert "probesets" to "genes"
Microarray
affy
limma
convert
Microarray
affy
limma
convert
updated 14.5 years ago by
Tobias Straub
▴ 430 • written 14.5 years ago by
Cheng-Yuan Kao
▴ 100
0
votes
6
replies
3.2k
views
converting probeset id to gene id's : fRMA
probe
affy
convert
frma
probe
affy
convert
frma
updated 9.9 years ago by
Peter Langfelder
★ 3.0k • written 9.9 years ago by
Abhishek Pratap
▴ 190
0
votes
6
replies
1.3k
views
writing a fasta file in blocks
probe
convert
probe
convert
updated 13.9 years ago by
Martin Morgan
25k • written 13.9 years ago by
Fahim Md
▴ 250
0
votes
6
replies
1.7k
views
BED2RangedData
GO
convert
GO
convert
updated 11.1 years ago by
R
▴ 40 • written 11.1 years ago by
Guest User
★ 13k
0
votes
6
replies
3.0k
views
DMR identification: minfi speed, memory problems
Annotation
convert
minfi
methyAnalysis
bumphunter
Annotation
convert
minfi
methyAnalysis
updated 10.2 years ago by
James W. MacDonald
65k • written 10.2 years ago by
Guest User
★ 13k
0
votes
6
replies
2.0k
views
String manipulation: String to Command
convert
convert
updated 18.6 years ago by
rgentleman
★ 5.5k • written 18.6 years ago by
Mohammad Esad-Djou
▴ 520
0
votes
6
replies
1.4k
views
arrayQualityMetrics error with MAList
convert
arrayQualityMetrics
convert
arrayQualityMetrics
updated 12.2 years ago by
Wolfgang Huber
★ 13k • written 12.2 years ago by
karen power
▴ 10
0
votes
6
replies
2.5k
views
IPI to entrez id
convert
convert
13.2 years ago
viritha kaza
▴ 580
2
votes
6
replies
1.6k
views
getLDS error in scan
biomaRt
getLDS
convert
gene symbols
updated 3.6 years ago by
Mike Smith
★ 6.5k • written 3.6 years ago by
mvis1231
• 0
0
votes
6
replies
1.1k
views
Gene names
convert
convert
updated 18.5 years ago by
Seth Falcon
★ 7.4k • written 18.5 years ago by
Narendra Kaushik
▴ 150
0
votes
6
replies
3.2k
views
LogFC query in Limma
Pathways
convert
Pathways
convert
updated 11.3 years ago by
Steve Lianoglou
★ 13k • written 11.3 years ago by
Roopa Subbaiaih
▴ 130
0
votes
5
replies
2.6k
views
summarizeOverlaps using GRanges or bed file as reads?
convert
convert
updated 10.1 years ago by
Martin Morgan
25k • written 10.1 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
5
replies
1.7k
views
A question about the function readGAlignmentPairs in GenomicRnages package
Alignment
Cancer
convert
GenomicAlignments
Alignment
Cancer
convert
GenomicAlignments
updated 10.1 years ago by
Hervé Pagès
16k • written 10.1 years ago by
Niu, Liang NIH/NIEHS [E]
▴ 50
0
votes
5
replies
1.2k
views
Boxplot from dataframe...
convert
convert
updated 18.3 years ago by
James W. MacDonald
65k • written 18.3 years ago by
David Ruau
▴ 110
0
votes
5
replies
1.5k
views
getBM (biomaRt) sometimes returns NULL
Annotation
limma
marray
convert
biomaRt
Annotation
limma
marray
convert
biomaRt
updated 18.1 years ago by
Wolfgang Huber
★ 13k • written 18.1 years ago by
Giovanni Coppola
▴ 250
0
votes
5
replies
3.0k
views
vsn: meanSdPlot + MAlist
Normalization
vsn
limma
convert
Normalization
vsn
limma
convert
updated 14.5 years ago by
Martin Morgan
25k • written 14.5 years ago by
Guido Hooiveld
★ 3.9k
0
votes
5
replies
2.1k
views
rhdf5 and factors
rhdf5
convert
rhdf5
convert
updated 11.3 years ago by
Bernd Fischer
▴ 550 • written 11.3 years ago by
Moritz E. Beber
▴ 10
0
votes
5
replies
1.9k
views
converting gene name to affy probe
probe
convert
biomaRt
probe
convert
biomaRt
16.0 years ago
Ruppert Valentino
▴ 270
0
votes
5
replies
3.1k
views
fastq files
convert
convert
updated 13.2 years ago by
Martin Morgan
25k • written 13.2 years ago by
David
▴ 860
0
votes
5
replies
1.7k
views
Help with promoter analysis
Transcription
convert
biomaRt
Transcription
convert
biomaRt
12.2 years ago
Davy
▴ 20
0
votes
5
replies
3.7k
views
how to convert genotype snp matrix to nucleotide genotypes?
SNP
convert
snpMatrix
SNP
convert
snpMatrix
updated 11.0 years ago by
Vincent J. Carey, Jr.
6.7k • written 11.0 years ago by
Tereza Jezkova UNLV
▴ 20
0
votes
5
replies
1.5k
views
deqseq_count and BWA-based SAM files
convert
DEXSeq
convert
DEXSeq
updated 12.4 years ago by
Shona Wood
▴ 70 • written 12.4 years ago by
Guest User
★ 13k
0
votes
5
replies
3.5k
views
Adjacency to network using R
Visualization
Network
convert
Visualization
Network
convert
updated 12.1 years ago by
Tim Triche
★ 4.2k • written 12.1 years ago by
pankaj borah
▴ 120
0
votes
5
replies
1.3k
views
from using biomaRt and r10kcod
r10kcod
probe
PROcess
convert
codelink
r10kcod
probe
PROcess
convert
codelink
updated 17.0 years ago by
Diego Diez
▴ 760 • written 17.0 years ago by
Weiwei Shi
★ 1.2k
0
votes
5
replies
804
views
Help on alternative and efficient data frame manipulation
convert
convert
updated 12.4 years ago by
Steve Lianoglou
★ 13k • written 12.4 years ago by
Julie Zhu
★ 4.3k
0
votes
5
replies
2.3k
views
Get Gene annotation (GO terms)
GO
convert
GO
convert
updated 13.1 years ago by
Marc Carlson
★ 7.2k • written 13.1 years ago by
David
▴ 860
0
votes
5
replies
2.1k
views
downloading different kinds of microarray data
Sequencing
Microarray
Genetics
Annotation
gpls
convert
GEOquery
GEOmetadb
Sequencing
gpls
updated 13.7 years ago by
Alex Levitchi
▴ 30 • written 13.7 years ago by
Sean Davis
21k
50 results • Page
1 of 1
Recent ...
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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