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Cancer
•
reset
6
votes
2
replies
3.5k
views
Is ComBat introducing a signal where there is none?
Microarray
Clustering
Cancer
limma
Microarray
Clustering
Cancer
limma
10.4 years ago • updated 8.7 years ago
Vegard Nygaard
▴ 110
6
votes
7
replies
1.3k
views
Appropriate experimental design for differential expresion
edgeR
normalization
cancer
updated 5.1 years ago by
swbarnes2
★ 1.3k • written 5.1 years ago by
AZ
▴ 30
4
votes
10
replies
2.5k
views
how to analyze WGCNA results?
cancer
probe
deseq2
annotation
normalization
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
rajpal22288
▴ 10
4
votes
1
reply
8.6k
views
WGCNA-unable to install GO.db package
go
cancer
updated 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
852108577
▴ 20
4
votes
7
replies
1.5k
views
Limma sample groups
microarray
limma
affy
cancer
updated 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
nancy.nassar1590
• 0
3
votes
1
reply
613
views
Gene expression analysis
cancer
R
updated 6.2 years ago by
James W. MacDonald
65k • written 6.2 years ago by
gladnovin
• 0
3
votes
0
replies
3.7k
views
biocLite() fails to install all limma dependencies from CRAN
Cancer
limma
Cancer
limma
17.0 years ago
Seth Falcon
★ 7.4k
3
votes
0
replies
2.6k
views
Job:
PhD opportunity in Cambridge (Computational Biology and Data Science)
cancer
deep learning
genomics
Job
computational biology
6.6 years ago • updated 6.5 years ago
Shamith.Samarajiwa
▴ 180
3
votes
0
replies
1.5k
views
Job:
PhD Positions in Computational Cancer Research
jobs
bioinformatics
biostatistics
cancer
next-generation sequencing
Job
8.0 years ago
Bernd Fischer
▴ 550
3
votes
0
replies
2.8k
views
Evidence-based guidelines for use the method="robust" option in lmFit
Microarray
Normalization
Bayesian
Regression
Cancer
limma
Microarray
Normalization
Cancer
13.0 years ago
Richard Friedman
★ 2.0k
3
votes
0
replies
1.2k
views
Job:
Postdoctoral Scientist position at intersection of Single-Cell Cancer Genomics, Data Science and Bioconductor Software Development
job
single-cell
data science
cancer
genomics
Job
5.3 years ago
Stephanie Hicks
▴ 80
3
votes
2
replies
3.5k
views
Limma and logistic regression
Microarray
Cancer
limma
Microarray
Cancer
limma
updated 14.2 years ago by
Claus Mayer
▴ 340 • written 14.2 years ago by
Daniel Brewer
★ 1.9k
2
votes
2
replies
1.4k
views
Solving error for error of factors
deseq2
cancer
R
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
dorothy.jrobbert
▴ 30
2
votes
0
replies
1.2k
views
Job:
Two Post-doctoral positions at the CRUK Cambridge Institute
cancer
methylation
rna-seq
Job
7.9 years ago
Andy Lynch
▴ 120
2
votes
2
replies
4.8k
views
Genecards v3 access
Cancer
Cancer
updated 13.7 years ago by
Sean Davis
21k • written 13.7 years ago by
Daniel Brewer
★ 1.9k
2
votes
3
replies
977
views
Batch correction for a sets of genes
cancer
deseq2
r
rnaseq
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
AZ
▴ 30
2
votes
4
replies
2.7k
views
makePdInfoPackage for Primeview arrays
BiocViews
Annotation
Cancer
Organism
cdf
probe
affy
biocViews
BiocViews
BiocViews
Cancer
updated 10.9 years ago by
cstrato
★ 3.9k • written 10.9 years ago by
Max Kauer
▴ 140
2
votes
13
replies
1.4k
views
Sample size imbalance in a multi-regional experiment
deseq2
cancer
updated 3.6 years ago by
Michael Love
41k • written 3.6 years ago by
bioconductor_user_1675
• 0
2
votes
5
replies
1.3k
views
obtaining a complete global alignment via pairwiseAlignment
Alignment
GO
Cancer
BSgenome
BSgenome
Alignment
GO
Cancer
BSgenome
BSgenome
updated 10.9 years ago by
Martin Morgan
25k • written 10.9 years ago by
Guest User
★ 13k
2
votes
4
replies
1.2k
views
SCAN.UPC : lost too many samples from GSE (BrainArray + ConvThreshold)
SCAN.UPC
probe
normalization
GEOdata
cancer
5.1 years ago
s.goncalvesclaro
▴ 10
2
votes
0
replies
2.2k
views
Job:
Job Opening: Computational Biologist @ Genentech Bioinformatics
Job
Sequencing
Genetics
Cancer
updated 9.6 years ago by
Dan Tenenbaum
★ 8.2k • written 9.7 years ago by
Michael Lawrence
★ 11k
2
votes
1
reply
1.3k
views
Best way to do quality control and analysis on Exon arrays
Annotation
Cancer
affy
exonmap
Annotation
Cancer
affy
exonmap
updated 8.8 years ago by
nicholaserho
▴ 10 • written 14.9 years ago by
Daniel Brewer
★ 1.9k
2
votes
1
reply
2.3k
views
How to perform a differential expression analysis from TCGA file EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv
cancer
limma
deseq2
updated 4.6 years ago by
svlachavas
▴ 830 • written 4.6 years ago by
KCLiv
▴ 20
2
votes
5
replies
1.8k
views
edgeR or wilcoxon rank test? Which is right?
edgeR
r
wilcox
RNA-seq
cancer
5.3 years ago
AZ
▴ 30
2
votes
5
replies
3.4k
views
Problem with BAM header in GAlignments
Cancer
Cancer
updated 10.3 years ago by
Martin Morgan
25k • written 10.3 years ago by
Taylor, Sean D
▴ 250
2
votes
0
replies
995
views
Job:
Research Fellow, Computational Cancer Genomics (University College London)
cancer
genomics
machine learning
data integration
multi-omics
Job
5.3 years ago
msecrier
▴ 20
2
votes
3
replies
1.2k
views
DESeq2: DE Analysis with very imbalanced samples per condition
deseq2
cancer
updated 3 months ago by
Shaimaa Gamal
• 0 • written 4.5 years ago by
thanos5541
• 0
1
vote
1
reply
1.0k
views
soggi average plot
soggi
multiple bam
cancer
updated 6.3 years ago by
kmezhoud
▴ 10 • written 6.3 years ago by
Wojeff
• 0
1
vote
0
replies
1.4k
views
Job:
UK/EU funded PhD Studentship: Detecting novel subtypes of cancer using data science and machine learning
PhD
clustering
cancer
Job
6.4 years ago • updated 6.1 years ago
Daniel Brewer
▴ 100
1
vote
0
replies
1.2k
views
Job:
Biomarker Data Analysis: Development of a Test for Prostate Cancer : PhD Studentship @ UEA, Norwich
phd
cancer
Job
7.0 years ago
Daniel Brewer
▴ 100
1
vote
0
replies
1.1k
views
Job:
Summer Vacation Studentships in Data Science, MRC Cancer Unit, University of Cambridge, UK
data science
data visualization
machine learning
cancer
Job
6.0 years ago • updated 5.9 years ago
Shamith.Samarajiwa
▴ 180
1
vote
0
replies
1.3k
views
Job:
Computational Biologist position in CRUK Manchester Institute, UK
bioinformatician job
ngs
leukemia
cancer
Job
7.9 years ago
Hui Sun Leong
▴ 10
1
vote
0
replies
1.1k
views
Job:
Summer Studentship in Data Science (Cancer Research) at the University of Cambridge
cancer
summer studentship
Job
7.9 years ago
Shamith.Samarajiwa
▴ 180
1
vote
0
replies
1.8k
views
Job:
PostDoc at Novartis Oncology Basel - Intratumor heterogeneity
cancer
genomics
postdoc
job
Job
8.0 years ago
Kauffmann, Audrey
▴ 60
1
vote
2
replies
2.4k
views
TCGAbiolinks data download problem
cancer
microarray
bioconductor
tcgabiolinks
8.0 years ago
Fernando
• 0
1
vote
4
replies
2.1k
views
How to install old GenomicRanges 1.14.4 package ?
bioconductor
R
cancer
probe
deseq2
updated 7.9 years ago by
derbecker
▴ 10 • written 8.0 years ago by
winter_li
• 0
1
vote
2
replies
3.7k
views
mixed model using limma-voom
limma
cancer
7.6 years ago
Yanzhu Lin
▴ 120
1
vote
2
replies
1.0k
views
genes repeated in the heatmap several times(10x) when using limma
limma
normalization
heatmap
design and contrast matrix
cancer
updated 5.5 years ago by
Axel Klenk
★ 1.0k • written 5.5 years ago by
andreilazar9
• 0
1
vote
0
replies
1.9k
views
Job:
Harvard Medical School Postdoc- The Center for Biomedical Informatics
cancer
genomic analysis
computational biology
Job
9.0 years ago
Doe, Aimee
▴ 40
1
vote
3
replies
2.2k
views
views on Rle using GRanges object
RNASeq
Coverage
GO
Cancer
bridge
rtracklayer
IRanges
RNASeq
Coverage
GO
Cancer
bridge
updated 10.1 years ago by
Hervé Pagès
16k • written 10.1 years ago by
Michael Lawrence
★ 11k
1
vote
1
reply
2.9k
views
DESeq2 plotPCA and scale
Cancer
Cancer
updated 9.8 years ago by
Michael Love
41k • written 9.8 years ago by
Daniel Brewer
▴ 100
1
vote
2
replies
2.3k
views
Job:
Postdoctoral Research Fellow in Bioinformatics – Systems Biology of Childhood Cancer
bioinformatics
systemsbiology
cancer
job
austria
Job
8.8 years ago • updated 8.7 years ago
heinrich.kovar
▴ 10
1
vote
5
replies
1.9k
views
'version' is missing error when running makeTxDbPackageFromUCSC
Cancer
TranscriptDb
IRanges
GenomicFeatures
Cancer
TranscriptDb
IRanges
GenomicFeatures
updated 8.5 years ago by
dave
▴ 10 • written 10.7 years ago by
Hervé Pagès
16k
1
vote
2
replies
1.6k
views
DESeq2: detect significantly increasing across an ordinal variable
RNASeq
Cancer
DESeq2
RNASeq
Cancer
DESeq2
updated 9.8 years ago by
Michael Love
41k • written 9.8 years ago by
Daniel Brewer
▴ 100
1
vote
1
reply
2.0k
views
Multifactor model design for DE analysis (DESeq2 & edgeR)
Cancer
edgeR
DESeq2
Cancer
edgeR
DESeq2
updated 9.7 years ago by
Simon Anders
★ 3.7k • written 9.7 years ago by
Mathieu Bahin
▴ 30
1
vote
1
reply
2.8k
views
Creat PWM from Alignment with Gaps
Alignment
Cancer
Alignment
Cancer
updated 10.6 years ago by
Lakshmanan Iyer
▴ 250 • written 10.6 years ago by
Hervé Pagès
16k
1
vote
0
replies
1.7k
views
Job:
Post-doc Position in Epigenetic Bioinformatics
cancer
sequencing
epigenetics
computational biology
bioinformatics
Job
8.5 years ago
Yassen Assenov
▴ 10
1
vote
1
reply
1.5k
views
Question about EAGenes (TCGAbiolinks)
annotation
cancer
biomart
genetics
R
updated 8.1 years ago by
Tiago Chedraoui Silva
▴ 260 • written 8.2 years ago by
pathkim
• 0
1
vote
0
replies
1.9k
views
pileup coverage from BAM file
Coverage
Cancer
IRanges
GenomicRanges
Coverage
Cancer
IRanges
GenomicRanges
11.2 years ago
Martin Morgan
25k
1
vote
3
replies
1.0k
views
distanceToNearest for GRanges?
Cancer
Cancer
updated 12.1 years ago by
Malcolm Cook
★ 1.6k • written 12.1 years ago by
Janet Young
▴ 740
50 results • Page
1 of 1
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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