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Sequencing
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0
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17k
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1000 R tutorials/Links
Sequencing
Microarray
Genetics
Visualization
Network
Bayesian
Classification
Clustering
13.8 years ago
David Lyon
▴ 340
0
votes
4
replies
8.0k
views
DESeq adjusted pvalue calculation / filtering data
Sequencing
Organism
qvalue
DESeq
Sequencing
Organism
qvalue
DESeq
updated 12.3 years ago by
Naomi Altman
★ 6.0k • written 12.4 years ago by
Markus Grohme
▴ 20
0
votes
6
replies
6.9k
views
DeSeq vs current version of Cuffdiff
Sequencing
Bayesian
Cancer
DESeq
Sequencing
Bayesian
Cancer
DESeq
updated 12.1 years ago by
Stephen Turner
▴ 290 • written 12.1 years ago by
Richard Friedman
★ 2.0k
2
votes
4
replies
6.8k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing
Alignment
DESeq
DESeq2
Sequencing
Alignment
DESeq
DESeq2
updated 8.8 years ago by
gaelgarcia
• 0 • written 9.8 years ago by
Guest User
★ 13k
0
votes
2
replies
6.3k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP
Sequencing
Coverage
Alignment
Cancer
Biostrings
PROcess
IRanges
GenomicRanges
SNP
updated 10.4 years ago by
Michael Lawrence
★ 11k • written 10.4 years ago by
Hervé Pagès
16k
0
votes
1
reply
6.2k
views
Missing SAM header?
sequencing
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
Chris Fenton
▴ 80
0
votes
2
replies
4.6k
views
gplots Heatmap
SNP
Transcription
Sequencing
RNASeq
miRNA
Microarray
Annotation
Normalization
GO
Cancer
updated 12.1 years ago by
Wolfgang Huber
★ 13k • written 12.1 years ago by
Polikepahad, Sumanth
▴ 10
3
votes
8
replies
4.4k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing
DESeq
Sequencing
DESeq
updated 7.6 years ago by
contactbiostructure
• 0 • written 10.3 years ago by
Guest User
★ 13k
0
votes
0
replies
4.0k
views
Bioconductor 2.14 is released
BiocViews
aCGH
SNP
Sequencing
RNASeq
ChIPSeq
miRNA
Microarray
qPCR
Metabolomics
Coverage
10.0 years ago
Dan Tenenbaum
★ 8.2k
0
votes
0
replies
4.0k
views
cpm cutoff (edgeR) [was: total count filter cutoff (edgeR)]
Sequencing
miRNA
edgeR
Sequencing
miRNA
edgeR
9.8 years ago
Gordon Smyth
50k
0
votes
0
replies
4.0k
views
Bioconductor 2.13 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
miRNA
Microarray
Genetics
Proteomics
Coverage
10.5 years ago
Dan Tenenbaum
★ 8.2k
0
votes
2
replies
3.8k
views
Bioconductor 2.12 is released
BiocViews
aCGH
SNP
Transcription
Sequencing
Microarray
Coverage
Alignment
Annotation
GO
updated 8.7 years ago by
marksteve952
• 0 • written 11.0 years ago by
Dan Tenenbaum
★ 8.2k
8
votes
2
replies
3.5k
views
Appropriate ways to filter counts data for voom/limma
limma
edger
sequencing
updated 7.6 years ago by
Gordon Smyth
50k • written 7.6 years ago by
blofeld
▴ 10
0
votes
14
replies
3.4k
views
Trimming of partial adaptor sequences
Sequencing
Cancer
Biostrings
Sequencing
Cancer
Biostrings
10.7 years ago
Taylor, Sean D
▴ 250
3
votes
4
replies
3.3k
views
Variance filtering prior to RNA-seq differential expression
sequencing
deseq
limma
updated 8.7 years ago by
Gordon Smyth
50k • written 8.7 years ago by
chris86
▴ 420
0
votes
3
replies
3.2k
views
mirDeep2 edgeR analysis
Sequencing
miRNA
microRNA
Sequencing
miRNA
microRNA
updated 10.6 years ago by
Ryan C. Thompson
★ 7.9k • written 10.6 years ago by
Flores Torres, Mariana
▴ 10
5
votes
2
replies
3.1k
views
Gviz - show plus and minus strand from a bam
Sequencing
Coverage
Gviz
Sequencing
Coverage
Gviz
updated 10.4 years ago by
florian.hahne@novartis.com
★ 1.6k • written 10.4 years ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
0
replies
3.1k
views
Bioconductor 2.11 is released
BiocViews
SNP
Transcription
Sequencing
miRNA
Microbiome
Microarray
qPCR
Genetics
Coverage
11.5 years ago
Dan Tenenbaum
★ 8.2k
6
votes
1
reply
3.0k
views
[ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids
Sequencing
Annotation
convert
biomaRt
ReportingTools
DESeq2
Sequencing
Annotation
convert
updated 9.2 years ago by
andrew.j.skelton73
▴ 370 • written 10.3 years ago by
Jason Hackney
▴ 160
0
votes
1
reply
3.0k
views
ChIPseeker: Error in annotatePeak
Sequencing
GO
annotate
ChIPseeker
Sequencing
GO
annotate
ChIPseeker
9.9 years ago
António Miguel de Jesus Domingues
▴ 490
1
vote
2
replies
3.0k
views
Interaction categorical/continuous variable DESeq2
Sequencing
DESeq2
updated 9.5 years ago by
Wolfgang Huber
★ 13k • written 9.5 years ago by
Hugo Varet
▴ 80
0
votes
2
replies
2.8k
views
DE analysis with reference transcriptome
Sequencing
GO
Organism
edgeR
DESeq
EBSeq
Sequencing
GO
Organism
edgeR
DESeq
EBSeq
updated 9.9 years ago by
James W. MacDonald
65k • written 9.9 years ago by
Nicole Ertl
▴ 10
3
votes
3
replies
2.8k
views
Clarrification of ReadDNAStringSet
sequencing
9.2 years ago
khouloud.madbouh
• 0
0
votes
4
replies
2.7k
views
DNAString: Standard checksum function?
Biostrings
FASTA
sequencing
8.1 years ago
Henrik Bengtsson
★ 2.4k
0
votes
7
replies
2.7k
views
[ReportingTools] and DESeq2 results, publish DESeqDataSet using resultsNames other than the default
Sequencing
ReportingTools
DESeq2
Sequencing
ReportingTools
DESeq2
updated 10.2 years ago by
James W. MacDonald
65k • written 10.2 years ago by
Dimitra Alexopoulou
▴ 30
0
votes
0
replies
2.6k
views
Postdoctoral position at Novartis, Basel
Sequencing
Microarray
Sequencing
Microarray
12.2 years ago
Kauffmann, Audrey
▴ 60
0
votes
13
replies
2.6k
views
multiple hits with countOverlaps function
Sequencing
GenomicFeatures
Sequencing
GenomicFeatures
13.0 years ago
Wei Shi
★ 3.6k
0
votes
17
replies
2.6k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing
RNASeq
Microarray
qPCR
Coverage
edgeR
DESeq
Sequencing
RNASeq
Microarray
qPCR
updated 10.9 years ago by
Steve Lianoglou
★ 13k • written 10.9 years ago by
Lucia Peixoto
▴ 330
1
vote
1
reply
2.6k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R
sequencing
alignment
rsamtools
mapping
updated 5.9 years ago by
James W. MacDonald
65k • written 5.9 years ago by
nginet
▴ 10
0
votes
0
replies
2.6k
views
Job:
Postdoc in Population Genomics - UC Davis
bioinformatics
evolution
sequencing
genome analysis
genomics
Job
5.5 years ago
hschmidt
• 0
0
votes
1
reply
2.5k
views
Large logCPM values when using offsets in edgeR for normalization
Sequencing
edgeR
cqn
EDASeq
Sequencing
edgeR
cqn
EDASeq
updated 11.0 years ago by
Gordon Smyth
50k • written 11.0 years ago by
Ying W
▴ 90
0
votes
9
replies
2.5k
views
MEDIPS: how does MEDIPS define a methylated region / cluster?
Sequencing
MEDIPS
updated 9.5 years ago by
mengru1223
• 0 • written 9.6 years ago by
Guest User
★ 13k
0
votes
2
replies
2.4k
views
BiomaRt and extracting genomic sequence
Sequencing
biomaRt
Sequencing
biomaRt
updated 15.2 years ago by
steffen@stat.Berkeley.EDU
▴ 600 • written 15.2 years ago by
RS Illingworth
▴ 10
0
votes
3
replies
2.4k
views
Create consensus fasta file from indexed Bam file
Sequencing
Sequencing
updated 10.8 years ago by
Hervé Pagès
16k • written 10.8 years ago by
Guest User
★ 13k
1
vote
0
replies
2.4k
views
dispersion in edgeR
Sequencing
edgeR
13.8 years ago • updated 21 months ago
Gordon Smyth
50k
1
vote
1
reply
2.4k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing
biostrings
shortread
updated 8.4 years ago by
Martin Morgan
25k • written 8.4 years ago by
steven.everman
▴ 10
0
votes
8
replies
2.3k
views
DEXSeq - too many exons in gene
Sequencing
Annotation
DEXSeq
Sequencing
Annotation
DEXSeq
updated 10.1 years ago by
Steve Lianoglou
★ 13k • written 10.1 years ago by
António Miguel de Jesus Domingues
▴ 490
0
votes
0
replies
2.3k
views
Open-rank faculty position, Dept of Biostatistics, Virginia Commonwealth University
Sequencing
Cancer
Sequencing
Cancer
11.5 years ago
Kellie J. Archer, Ph.D.
▴ 120
0
votes
9
replies
2.3k
views
SOLiD color space data
Sequencing
Sequencing
updated 13.3 years ago by
rcaloger
▴ 500 • written 13.3 years ago by
Neel Aluru
▴ 460
0
votes
2
replies
2.3k
views
edgeR question tags per million
Sequencing
Sequencing
updated 13.8 years ago by
Mark Robinson
★ 1.1k • written 13.8 years ago by
David
▴ 860
3
votes
1
reply
2.2k
views
Adjusting for gender using limma
limma
microarray
sequencing
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
chris86
▴ 420
2
votes
0
replies
2.2k
views
Job:
Job Opening: Computational Biologist @ Genentech Bioinformatics
Job
Sequencing
Genetics
Cancer
updated 9.5 years ago by
Dan Tenenbaum
★ 8.2k • written 9.6 years ago by
Michael Lawrence
★ 11k
4
votes
2
replies
2.2k
views
Detect global differences in miRNA expression between tumor and normal using spike-ins
edger
limma
mirna
sequencing
updated 8.7 years ago by
Aaron Lun
★ 28k • written 8.7 years ago by
R
▴ 40
0
votes
7
replies
2.2k
views
Bioconductor 2.6 is released
Sequencing
Microarray
Visualization
Infrastructure
PROcess
beadarray
keggorthology
eisa
updated 7.6 years ago by
wangyizhusss
• 0 • written 13.9 years ago by
Patrick Aboyoun
★ 1.6k
0
votes
0
replies
2.2k
views
Two bioinformatics positions in Bordeaux, France
SNP
Sequencing
Genetics
Cancer
Breast
SNP
Sequencing
Genetics
Cancer
Breast
13.9 years ago
Audrey Kauffmann
▴ 110
0
votes
0
replies
2.2k
views
Rsubread featureCounts unexpected strand-specifc counts with Ensembl GTF
Sequencing
Annotation
9.6 years ago
Wei Shi
★ 3.6k
1
vote
1
reply
2.2k
views
Perplexing results with Limma with RNA-seq data
sequencing
microarray
updated 8.6 years ago by
Steve Lianoglou
★ 13k • written 8.6 years ago by
chris86
▴ 420
0
votes
0
replies
2.2k
views
featureCounts read summarization function
Sequencing
Annotation
Rsubread
Sequencing
Annotation
Rsubread
10.7 years ago
Wei Shi
★ 3.6k
0
votes
5
replies
2.2k
views
getting sample size for RNAseq experiment
rnaseqpower
sspa
sample size
sequencing
complex-design
updated 8.1 years ago by
m.van_iterson
▴ 20 • written 8.1 years ago by
roser.navarro
• 0
0
votes
0
replies
2.1k
views
Differential gene expression: EdgeR / DESeq and identifying noise/outliers
Sequencing
edgeR
DESeq
Sequencing
edgeR
DESeq
11.8 years ago
Michael Salbaum
▴ 80
50 results • Page
1 of 1
Recent ...
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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