Showing : Cancer • reset
1
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pileup coverage from BAM file
Coverage Cancer IRanges GenomicRanges Coverage Cancer IRanges GenomicRanges
12.8 years ago Martin Morgan 25k
0
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0
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2.0k
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Conversion of minfi format MethylSet to methyAnalysis format MethyGenoSet
Cancer charm minfi methyAnalysis Cancer charm minfi methyAnalysis
12.8 years ago Ed Schwalbe ▴ 20
0
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0
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1.0k
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question about how to get ranges in Biostrings
Cancer IRanges Gviz Cancer IRanges Gviz
12.8 years ago Hervé Pagès 16k
0
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0
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1.2k
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Biostrings
GO Cancer Biostrings cycle GO Cancer Biostrings cycle
12.8 years ago Hervé Pagès 16k
0
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1
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2.5k
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Bioconductor Digest, Vol 120, Issue 12
Microarray qPCR Coverage Annotation Pathways Visualization Cancer Breast Organism affy
12.8 years ago Matthew Thornton ▴ 390
0
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3
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1.5k
views
speed of runmed on SimpleRleList
Coverage Cancer Coverage Cancer
updated 12.8 years ago by 16k • written 12.8 years ago by ▴ 740
0
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0
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989
views
New course material: Intermediate R / Bioc for High-Throughput Sequence Analysis
Annotation Visualization Cancer Annotation Visualization Cancer
12.8 years ago Martin Morgan 25k
0
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0
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1.0k
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Extract Exon Features from GenomicFeatures Leads to Inconsistent Pairing of Gene and Exon IDs
Cancer GenomicFeatures Cancer GenomicFeatures
12.8 years ago Hervé Pagès 16k
0
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0
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1.9k
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Job openings at Barts Cancer Institute, QMUL: Postdoctoral Research assistant and Bioinformatician
Sequencing Cancer Breast Sequencing Cancer Breast
12.8 years ago Claude Chelala ▴ 40
0
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0
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1.8k
views
[Course] CSAMA 2013: Computational Statistics for Genome Biology (11th edition) Brixen, Italy, June 24-28th 2013
Sequencing Epigenetics Cancer Sequencing Epigenetics Cancer
12.8 years ago stefano iacus ▴ 430
0
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1
reply
3.7k
views
a diffBind problem
Cancer edgeR DiffBind Cancer edgeR DiffBind
12.8 years ago Rory Stark ★ 5.2k
0
votes
13
replies
2.9k
views
statistical test for time course data
Cancer limma edgeR Cancer limma edgeR
updated 12.8 years ago by 53k • written 12.8 years ago by ▴ 260
0
votes
2
replies
1.5k
views
LogFC query in Limma
Pathways Cancer probe limma convert Pathways Cancer probe limma convert
updated 12.8 years ago by 53k • written 12.8 years ago by ▴ 130
0
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0
replies
778
views
Course reminder: Intermediate R / Bioc for Sequence Analysis
Cancer Cancer
12.8 years ago Martin Morgan 25k
0
votes
1
reply
857
views
Best Package To Normalize Microarray Data with Few Samples
Microarray Cancer Microarray Cancer
updated 12.9 years ago by ★ 4.2k • written 12.8 years ago by ▴ 230
0
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2
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1.8k
views
[devteam-bioc] Can you give me a sample to calculate the Read Depth with Rsamtools?
Coverage Cancer Rsamtools Coverage Cancer Rsamtools
updated 12.9 years ago by ▴ 10 • written 12.9 years ago by 25k
0
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6
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3.6k
views
about ComBat plot for non parametric
Microarray Cancer Microarray Cancer
updated 12.9 years ago by ▴ 30 • written 12.9 years ago by ▴ 870
0
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0
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1.0k
views
Error - BSgenomeForge function
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
12.9 years ago Hervé Pagès 16k
0
votes
4
replies
902
views
Limma and XML
Cancer Cancer
updated 12.9 years ago by 53k • written 12.9 years ago by ▴ 20
0
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0
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1.2k
views
Course: Intermediate R / Bioconductor for High-Throughput Sequence Analysis, 14-15 Feb, Seattle
Cancer Cancer
12.9 years ago Martin Morgan 25k
0
votes
0
replies
1.0k
views
Error installing iFlow (Jaques Fattaccioli)
Cancer iFlow BiocInstaller Cancer iFlow BiocInstaller
12.9 years ago Finak, Greg ▴ 40
0
votes
1
reply
1.3k
views
AffylmGUI freezes with recent updates of Windows 7 Enterprise Service Pack 1
Cancer affylmGUI Cancer affylmGUI
updated 12.9 years ago by ▴ 450 • written 12.9 years ago by ★ 2.0k
0
votes
0
replies
806
views
Bos taurus genome
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
12.9 years ago Hervé Pagès 16k
0
votes
0
replies
658
views
reducing hits from countGenomicOverlaps()
Cancer Cancer
12.9 years ago Michael Lawrence ★ 11k
0
votes
0
replies
950
views
Computer for the analysis of high-throughput genomic data
Sequencing Microarray GO Network Cancer Sequencing Microarray GO Network Cancer
12.9 years ago Steve Lianoglou ★ 13k
0
votes
28
replies
3.8k
views
countMatches() (was: table for GenomicRanges)
Cancer IRanges Cancer IRanges
updated 12.9 years ago by ★ 11k • written 12.9 years ago by 16k
0
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2
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1.6k
views
normalise many cel files TCBB-2007-11-0161_noCEL.tar
Cancer Homo sapiens affy Cancer Homo sapiens affy
updated 12.9 years ago by ▴ 20 • written 12.9 years ago by 25k
0
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0
replies
1.9k
views
Error message with transcriptCounts(easyRNASeq) performed with gtf file generated with cuffmerge
RNASeq Annotation Normalization Cancer Organism BSgenome BSgenome easyRNASeq RNASeq
12.9 years ago Richard Friedman ★ 2.0k
0
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3
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2.4k
views
Error: package/namespace load failed for ‘affycoretools
GO GUI Cancer GO GUI Cancer
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ★ 2.0k
0
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0
replies
1.6k
views
Why does a call to "unique" removes a DNAStringSet names?
Cancer Cancer
13.0 years ago Hervé Pagès 16k
0
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1
reply
1.3k
views
edgeR 3.0.6: Possible (small) bug in glmLRT when passing contrasts?
Cancer edgeR Cancer edgeR
updated 13.0 years ago by 53k • written 13.0 years ago by ▴ 30
0
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0
replies
1.3k
views
Job postings - computational biologists in translational science
Sequencing Cancer Sequencing Cancer
13.0 years ago Crispin Miller ★ 1.1k
0
votes
4
replies
1.4k
views
question about TranscriptDb
Cancer Cancer
updated 13.0 years ago by ★ 7.2k • written 13.0 years ago by ▴ 20
0
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1
reply
1.1k
views
Fwd: all human gene coordinates
Cancer Cancer
updated 13.0 years ago by ▴ 440 • written 13.0 years ago by ★ 13k
0
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1
reply
1.3k
views
filter low expression tags
Cancer Cancer
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 40
0
votes
7
replies
2.9k
views
Getting counts for previously undetected transcripts and genes with easyRNASeq: comparison to Cufflinks
RNASeq Annotation Cancer edgeR cqn easyRNASeq RNASeq Annotation Cancer edgeR cqn
updated 13.0 years ago by ★ 1.2k • written 13.0 years ago by ★ 2.0k
0
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8
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2.6k
views
IRanges/List oddity: do.call of `c` on a list of IRangesList returns "list" only when the list is named
Cancer IRanges BiocGenerics Cancer IRanges BiocGenerics
updated 13.0 years ago by ★ 11k • written 13.0 years ago by 16k
0
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0
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1.0k
views
readAligned with bowtie2 input
Alignment Cancer ShortRead Alignment Cancer ShortRead
13.0 years ago Martin Morgan 25k
0
votes
0
replies
1.5k
views
Error: cannot allocate vector of size 618.0 Mb
Annotation Cancer cdf Annotation Cancer cdf
13.0 years ago Henrik Bengtsson ★ 2.4k
0
votes
5
replies
2.0k
views
EBcoexpress error - initializeHP() error
Microarray Cancer EBcoexpress Microarray Cancer EBcoexpress
updated 13.0 years ago by ★ 8.2k • written 13.0 years ago by ★ 13k
0
votes
4
replies
1.9k
views
AnnotationForge example does not work
GO Cancer ChipName probe affy GO Cancer ChipName probe affy
updated 13.0 years ago by ▴ 120 • written 13.0 years ago by ★ 13k
0
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2
replies
1.6k
views
error message with easyRNASeq use case
RNASeq Cancer Organism easyRNASeq RNASeq Cancer Organism easyRNASeq
updated 13.0 years ago by 68k • written 13.0 years ago by ★ 2.0k
0
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3
replies
3.5k
views
Subsetting expression sets for mass spec data - second ask
Classification Cancer PROcess Classification Cancer PROcess
updated 13.0 years ago by 21k • written 13.0 years ago by ▴ 300
0
votes
3
replies
1.9k
views
limma design (paired and factorial?)
Cancer Prostate limma Cancer Prostate limma
updated 13.0 years ago by 53k • written 13.0 years ago by ▴ 30
0
votes
2
replies
879
views
limma: instances of highly variable paired ratios, but very small p-values
Cancer limma Cancer limma
updated 13.0 years ago by ▴ 20 • written 13.0 years ago by 53k
0
votes
6
replies
2.3k
views
Bioc packages not working with R2.15.2?
Cancer oligo Cancer oligo
updated 13.0 years ago by ★ 4.3k • written 13.1 years ago by ▴ 170
0
votes
0
replies
583
views
limma: instances of highly variable paired ratios, but very small p-values
Cancer limma Cancer limma
13.1 years ago Ryan Basom ▴ 20
0
votes
3
replies
2.4k
views
Error: 'devel' version requires a more recent R
GUI Cancer easyRNASeq GUI Cancer easyRNASeq
updated 13.1 years ago by 21k • written 13.1 years ago by ★ 2.0k
0
votes
0
replies
1.8k
views
Classification in Mass Spectrometry Data
Microarray Classification Cancer Ovarian PROcess MLInterfaces ASSIGN Microarray Cancer
13.1 years ago McGee, Monnie ▴ 300
0
votes
0
replies
1.3k
views
Bioinformatics job posting
Sequencing Cancer Sequencing Cancer
13.1 years ago Yinyin Yuan ▴ 10
1,555 results • Page 7 of 32
Recent ...
Replies
Comment: 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/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
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
Comment: upstream git branches of bioc-release
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Popular Question to jared.andrews07 ▴ 30
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