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Cancer
•
reset
0
votes
0
replies
747
views
BioC2012: upcoming deadlines
Cancer
Cancer
13.5 years ago
Martin Morgan
25k
0
votes
2
replies
942
views
[ChIPpeakAnno] Can not start ChIPpeakAnno after update to version 2.5.9
GO
Cancer
GO
Cancer
updated 13.5 years ago by
Dan Tenenbaum
★ 8.2k • written 13.5 years ago by
Martin Morgan
25k
0
votes
3
replies
3.2k
views
Is it possible to read in Bluefuse and Agilent files together using read.maimages() function in limma?
Cancer
Cancer
updated 13.5 years ago by
Gordon Smyth
53k • written 13.5 years ago by
Parisa Razaz
▴ 40
0
votes
1
reply
4.3k
views
samtools error
Cancer
convert
Cancer
convert
updated 13.5 years ago by
Lucia Peixoto
▴ 330 • written 13.5 years ago by
Marcus Davy
▴ 390
0
votes
1
reply
903
views
how to load RangedData for all chromosomes in one tab in UCSC browser using browserView from rtracklayer
GO
Cancer
rtracklayer
GO
Cancer
rtracklayer
updated 13.5 years ago by
Steve Lianoglou
★ 13k • written 13.5 years ago by
Yue Li
▴ 370
0
votes
0
replies
1.4k
views
build/check reports for ENVISIONQuery, IdMappingRetrieval on OSX
Cancer
RWebServices
SJava
CoGAPS
CRImage
Rsubread
Cancer
RWebServices
SJava
CoGAPS
13.5 years ago
Day, Roger S
▴ 60
0
votes
0
replies
1.1k
views
aCGH package. Plots: X axis label problems
aCGH
Cancer
aCGH
aCGH
Cancer
aCGH
13.5 years ago
Sarah JugurnauthLittle
▴ 20
0
votes
13
replies
2.7k
views
PWMscoreStartingAt and ambiguous subject seqs
Cancer
Biostrings
GLAD
Cancer
Biostrings
GLAD
updated 13.5 years ago by
Hervé Pagès
16k • written 13.5 years ago by
Janet Young
▴ 740
0
votes
0
replies
1.0k
views
ChIPpeakAnno annotatePeakInBatch
Cancer
Cancer
13.6 years ago
Julie Zhu
★ 4.3k
0
votes
9
replies
2.5k
views
necessity of moderated t statistic and false discoveries for small predefined gene list?
Cancer
affy
limma
Cancer
affy
limma
updated 13.6 years ago by
Moshe Olshansky
▴ 260 • written 13.6 years ago by
Richard Friedman
★ 2.0k
0
votes
1
reply
896
views
BSgenome packages for ce10 and panTro3 (was Re: BSgenome.Celegans.UCSC.cd10 for WS220)
Cancer
BSgenome
BSgenome
Cancer
BSgenome
BSgenome
updated 13.6 years ago by
Julie Zhu
★ 4.3k • written 13.6 years ago by
Hervé Pagès
16k
0
votes
2
replies
1.2k
views
question about BSgenome and C.pombe genome, absent in USCS
Cancer
BSgenome
BSgenome
Cancer
BSgenome
BSgenome
updated 13.6 years ago by
Henry Paik
▴ 30 • written 13.6 years ago by
Hervé Pagès
16k
0
votes
2
replies
1.3k
views
FW: miRNA annotation
miRNA
Annotation
GO
Cancer
miRNA
Annotation
GO
Cancer
updated 13.6 years ago by
James W. MacDonald
68k • written 13.6 years ago by
Wu, Huiyun
▴ 70
0
votes
2
replies
1.2k
views
Re-send directly to BioC on miRNA annoation
miRNA
Annotation
Cancer
miRNA
Annotation
Cancer
updated 13.6 years ago by
Valerie Obenchain
★ 6.8k • written 13.6 years ago by
Wu, Huiyun
▴ 70
0
votes
0
replies
1.2k
views
Question regarding MADE4 graphs
Cancer
made4
Cancer
made4
13.6 years ago
Aedin Culhane
▴ 510
0
votes
1
reply
1.9k
views
Copy Number Analysis across multiple SNP array plaforms
SNP
Cancer
crlmm
ffpe
SNP
Cancer
crlmm
ffpe
updated 13.6 years ago by
Djork Clevert
▴ 210 • written 13.6 years ago by
Ed Schwalbe
▴ 20
0
votes
0
replies
1.2k
views
Help strange GSEA error
Cancer
Cancer
13.6 years ago
Martin Morgan
25k
0
votes
0
replies
677
views
combining hgu133a and hgu133b
Cancer
cdf
Cancer
cdf
13.6 years ago
Steve Lianoglou
★ 13k
0
votes
4
replies
4.3k
views
supervised & unsupervised analysis of samples of microarray data
Cancer
Cancer
updated 13.6 years ago by
Steve Lianoglou
★ 13k • written 13.6 years ago by
wenhuo hu
▴ 200
0
votes
0
replies
912
views
DESeq error thrown during estimateDispersions w/ coxReid method
Cancer
DEXSeq
Cancer
DEXSeq
13.6 years ago
Steve Lianoglou
★ 13k
0
votes
1
reply
1.7k
views
FW: Overlay Gene Expression on SNP (copy number) data
SNP
Coverage
Network
Cancer
TranscriptDb
IRanges
RCytoscape
ggbio
Gviz
SNP
Coverage
updated 13.6 years ago by
Tim Triche
★ 4.2k • written 13.6 years ago by
Ekta Jain
▴ 370
0
votes
1
reply
1.9k
views
Some particulars about rtracklayer::liftOver
Cancer
rtracklayer
Cancer
rtracklayer
updated 13.6 years ago by
Michael Lawrence
★ 11k • written 13.6 years ago by
Steve Lianoglou
★ 13k
0
votes
3
replies
1.8k
views
Gene-gene interaction analysis
Cancer
Cancer
updated 13.6 years ago by
Tengfei Yin
▴ 420 • written 13.6 years ago by
Yadav Sapkota
▴ 130
0
votes
7
replies
1.7k
views
distanceToNearest for GRanges?
Cancer
GenomicRanges
Cancer
GenomicRanges
updated 13.6 years ago by
Michael Muratet
▴ 420 • written 13.7 years ago by
Valerie Obenchain
★ 6.8k
0
votes
2
replies
2.0k
views
Calculating alignment scores from aligned sequences
Alignment
Cancer
Biostrings
Alignment
Cancer
Biostrings
updated 13.6 years ago by
Michael Lawrence
★ 11k • written 13.6 years ago by
Steve Lianoglou
★ 13k
0
votes
3
replies
1.3k
views
Parallelizing Biostrings::pairwiseAlignment locally with multicore::mclapply problems?
Cancer
Cancer
13.6 years ago
Steve Lianoglou
★ 13k
0
votes
0
replies
1.7k
views
[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer
Organism
biomaRt
genomes
Cancer
Organism
biomaRt
genomes
13.7 years ago
Malcolm Cook
★ 1.6k
0
votes
1
reply
1.1k
views
Question about using lumi package
Cancer
lumi
Cancer
lumi
updated 13.7 years ago by
Pan Du
▴ 440 • written 13.7 years ago by
Hu, Xin
▴ 10
0
votes
0
replies
1.3k
views
Bioconductor Digest, Vol 110, Issue 11
Normalization
Cancer
lumi
methylumi
Normalization
Cancer
lumi
methylumi
13.7 years ago
Pan Du
▴ 440
0
votes
1
reply
1.9k
views
Errors for estimateGLMTrendedDisp and estimateGLMCommonDisp functions in the edgeR package
Cancer
edgeR
Cancer
edgeR
updated 13.7 years ago by
Gordon Smyth
53k • written 13.7 years ago by
Yao,Hui
▴ 40
0
votes
1
reply
1.2k
views
Course: R / Bioconductor for High-Throughput Sequence Analysis
Annotation
Cancer
genomes
Annotation
Cancer
genomes
13.7 years ago
Martin Morgan
25k
0
votes
0
replies
908
views
oligonucleotideTransitions from Biostrings package
Cancer
Biostrings
Cancer
Biostrings
13.7 years ago
Hervé Pagès
16k
1
vote
3
replies
1.4k
views
distanceToNearest for GRanges?
Cancer
Cancer
updated 13.7 years ago by
Malcolm Cook
★ 1.6k • written 13.7 years ago by
Janet Young
▴ 740
0
votes
8
replies
2.3k
views
Problems using arrayQualityMetrics
Cancer
arrayQualityMetrics
Cancer
arrayQualityMetrics
13.7 years ago
Rosalind Cutts
▴ 20
0
votes
0
replies
1.5k
views
JOB: Research Associate in Statistical Epigenomics (London)
Cancer
Ovarian
PROcess
Cancer
Ovarian
PROcess
13.7 years ago
Andrew Teschendorff
▴ 60
0
votes
6
replies
2.0k
views
[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer
Organism
biomaRt
GenomicFeatures
genomes
Cancer
Organism
biomaRt
GenomicFeatures
updated 13.7 years ago by
Rhoda Kinsella
▴ 660 • written 13.7 years ago by
Hervé Pagès
16k
0
votes
0
replies
1.5k
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation
GO
Cancer
Apis mellifera
BSgenome
Biostrings
Category
BSgenome
rtracklayer
GO
13.7 years ago
Matthew Young
▴ 50
0
votes
0
replies
1.2k
views
post-doctoral position
Cancer
Cancer
13.7 years ago
Day, Roger S
▴ 60
0
votes
1
reply
908
views
Intersecting two chromosomal ranges but keeping the unique ones
Cancer
Cancer
updated 13.7 years ago by
Yadav Sapkota
▴ 130 • written 13.7 years ago by
Steve Lianoglou
★ 13k
0
votes
5
replies
1.4k
views
A few Q's on using DEXSeq with mucho data
Cancer
DEXSeq
Cancer
DEXSeq
updated 13.7 years ago by
Simon Anders
★ 3.8k • written 13.7 years ago by
Steve Lianoglou
★ 13k
0
votes
3
replies
1.8k
views
homopolymer gap extension penalty in Biostrings
Sequencing
Alignment
GO
Cancer
Sequencing
Alignment
GO
Cancer
updated 13.8 years ago by
Noah Hoffman
▴ 10 • written 13.8 years ago by
Hervé Pagès
16k
0
votes
0
replies
864
views
report a possible bug of
Cancer
ShortRead
Cancer
ShortRead
13.8 years ago
Martin Morgan
25k
0
votes
1
reply
1.0k
views
countOverlaps within Mode Counting
Cancer
Cancer
updated 13.8 years ago by
Dario Strbenac
★ 1.6k • written 13.8 years ago by
Valerie Obenchain
★ 6.8k
0
votes
0
replies
1.2k
views
PostForm() with KEGG
GO
Cancer
KEGGSOAP
GO
Cancer
KEGGSOAP
13.8 years ago
Voke AO
▴ 760
0
votes
3
replies
6.4k
views
how to get gene list for given GO terms?
Pathways
GO
Cancer
PROcess
goTools
genomes
Pathways
GO
Cancer
PROcess
goTools
genomes
updated 3.4 years ago by
pengmin.wang.1
• 0 • written 13.8 years ago by
Marc Carlson
★ 7.2k
0
votes
0
replies
1.0k
views
cutoff for NUSE plot in oligo
Cancer
Cancer
13.8 years ago
Richard Friedman
★ 2.0k
0
votes
0
replies
755
views
adding factors to a data frame from a dataframe
GO
Cancer
GO
Cancer
13.8 years ago
Tom Keller
▴ 70
0
votes
0
replies
1.4k
views
Updated affy package? ReadAffy/ AffyBatch has changed and breaks my pipeline!
Cancer
cdf
probe
affy
gcrma
AnnotationDbi
Cancer
cdf
probe
affy
gcrma
AnnotationDbi
13.8 years ago
Benjamin Otto
▴ 830
0
votes
0
replies
1.1k
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation
GO
Cancer
Apis mellifera
BSgenome
Biostrings
BSgenome
rtracklayer
goseq
GO
13.8 years ago
Alicia Oshlack
▴ 100
0
votes
0
replies
1.0k
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation
GO
Cancer
BSgenome
Biostrings
BSgenome
rtracklayer
GenomicFeatures
goseq
GO
13.8 years ago
Hervé Pagès
16k
1,555 results • Page
9 of 32
Recent ...
Replies
Comment: GOseq Probability Weight Function bad fit
by
ejasge.r.m
• 0
When performing GO analysis with GOseq, i s important to carefully check your input and assumptions, just like reviewing choices on the McD…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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68k
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