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Showing :
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 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
rajpal22288
▴ 10
4
votes
1
reply
8.5k
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
612
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
2.7k
views
Evidence-based guidelines for use the method="robust" option in lmFit
Microarray
Normalization
Bayesian
Regression
Cancer
limma
Microarray
Normalization
Cancer
12.9 years ago
Richard Friedman
★ 2.0k
3
votes
0
replies
1.1k
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 14.1 years ago by
Claus Mayer
▴ 340 • written 14.1 years ago by
Daniel Brewer
★ 1.9k
2
votes
2
replies
1.4k
views
Solving error for error of factors
deseq2
cancer
R
updated 6.6 years ago by
Michael Love
41k • written 6.6 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 13.6 years ago by
Sean Davis
21k • written 13.6 years ago by
Daniel Brewer
★ 1.9k
2
votes
3
replies
974
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
1.3k
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 8.7 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
5.2 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
989
views
Job:
Research Fellow, Computational Cancer Genomics (University College London)
cancer
genomics
machine learning
data integration
multi-omics
Job
5.2 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 4.4 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
2.0k
views
How to install old GenomicRanges 1.14.4 package ?
bioconductor
R
cancer
probe
deseq2
updated 7.9 years ago by
derbecker
▴ 10 • written 7.9 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
2.2k
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 10.5 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
8.4 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 8.1 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
998
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
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Replies
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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