Showing : Cancer • reset
0
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4
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1.3k
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selecting score(GRanges_object) based on coordinates
Cancer Cancer
11.8 years ago Philip Lijnzaad ▴ 160
0
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3
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2.6k
views
limma and Volcano Plots
Microarray Proteomics Cancer PROcess Microarray Proteomics Cancer PROcess
updated 11.8 years ago by 53k • written 11.8 years ago by ▴ 130
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1
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1.0k
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Tool inqured to analysis array expression and cell line screening data
Cancer Cancer
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ★ 13k
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0
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3.8k
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Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
11.9 years ago Elena Serrano ▴ 30
0
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1
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1.6k
views
I need help making a dcf seed file to encapsulate a genome assembly im using.
Cancer Yeast BSgenome BSgenome Cancer Yeast BSgenome BSgenome
updated 11.9 years ago by ▴ 10 • written 11.9 years ago by 16k
0
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4
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1.9k
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AllelicImbalance with VCFs?
RNASeq Cancer trio AllelicImbalance RNASeq Cancer trio AllelicImbalance
updated 11.9 years ago by ▴ 20 • written 11.9 years ago by ▴ 10
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0
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1.9k
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EximiR - Limma - miRCURY LNA - Exiqon
miRNA Microarray Cancer limma lumi ExiMiR miRNA Microarray Cancer limma lumi ExiMiR
11.9 years ago Paolo Kunderfranco ▴ 350
2
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5
replies
3.9k
views
Problem with BAM header in GAlignments
Cancer Cancer
updated 11.9 years ago by 25k • written 11.9 years ago by ▴ 250
0
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0
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1.5k
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Job opening: Staff Scientist – Computational Biology and Bioinformatics – Massachusetts General Hospital, Boston, MA, USA
Sequencing Microarray Cancer Sequencing Microarray Cancer
11.9 years ago Wittner, Ben ▴ 290
0
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0
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1.4k
views
ensemblVEP, variant_effect_predictor versions and release schedule
Cancer MLInterfaces bridge ensemblVEP AnnotationHub Cancer MLInterfaces bridge ensemblVEP
11.9 years ago Valerie Obenchain ★ 6.8k
0
votes
1
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1.9k
views
Error message using arrayweights
GO Cancer mouse4302 KEGGREST GO Cancer mouse4302 KEGGREST
updated 12.0 years ago by ▴ 1000 • written 12.0 years ago by ▴ 80
0
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0
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2.0k
views
Easy way to convert CharacterList to character, collapsing each element?
Annotation Cancer Biostrings IRanges Annotation Cancer Biostrings IRanges
12.0 years ago Hervé Pagès 16k
0
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1
reply
5.8k
views
Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS
updated 12.0 years ago by ▴ 280 • written 12.0 years ago by 16k
0
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0
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615
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New Seattle Bioconductor group members
Cancer Cancer
12.0 years ago Martin Morgan 25k
0
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0
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2.3k
views
Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome GO
12.0 years ago Hervé Pagès 16k
0
votes
0
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2.4k
views
BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS
12.0 years ago Hervé Pagès 16k
0
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0
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1.9k
views
Job: Postdoc positions - Computational Biology - Center for Genomic Science, Milan, Italy
Sequencing Cancer Sequencing Cancer
12.0 years ago mattia pelizzola ▴ 200
0
votes
2
replies
1.1k
views
Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction
Cancer Cancer
updated 12.0 years ago by ★ 1.6k • written 12.0 years ago by ▴ 740
0
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2
replies
1.5k
views
ggbio tracks with labelled: problem when I add a main title
Cancer ggbio Cancer ggbio
12.0 years ago Janet Young ▴ 740
0
votes
16
replies
5.1k
views
subset a RleList using GRanges object?
Coverage Cancer IRanges Coverage Cancer IRanges
updated 12.0 years ago by 16k • written 12.0 years ago by ▴ 740
0
votes
0
replies
869
views
BSgenome.Mmulatta.UCSC
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
12.0 years ago Hervé Pagès 16k
0
votes
5
replies
1.9k
views
Query on ChipPeakAnno: AnnotatePeakinBatch input
Annotation Cancer ChIPpeakAnno Annotation Cancer ChIPpeakAnno
updated 12.0 years ago by ▴ 30 • written 12.0 years ago by ★ 4.3k
0
votes
1
reply
1.8k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges Rsubread easyRNASeq GO
updated 12.0 years ago by ▴ 320 • written 12.0 years ago by 53k
0
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0
replies
1.5k
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easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges easyRNASeq Coverage GO
12.0 years ago Nicolas Delhomme ▴ 320
0
votes
1
reply
2.5k
views
Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
updated 12.0 years ago by ★ 4.3k • written 12.0 years ago by ▴ 290
0
votes
1
reply
1.1k
views
ComBat
Cancer Cancer
updated 12.1 years ago by ★ 3.0k • written 12.1 years ago by ▴ 20
0
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2
replies
1.6k
views
segfault ReadAffy cause 'memory not mapped'
Cancer hgu133plus2 affy PROcess Cancer hgu133plus2 affy PROcess
updated 12.1 years ago by ★ 1.2k • written 12.1 years ago by ▴ 70
0
votes
2
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7.3k
views
how to obtain base counts from BAM file at specific genomic coordinates
SNP Sequencing Coverage Alignment Cancer Biostrings PROcess IRanges GenomicRanges SNP
updated 12.1 years ago by ★ 11k • written 12.1 years ago by 16k
0
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0
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1.2k
views
A question when using Biostrings
Cancer Biostrings Cancer Biostrings
12.1 years ago Hervé Pagès 16k
1
vote
1
reply
3.4k
views
Creat PWM from Alignment with Gaps
Alignment Cancer Alignment Cancer
updated 12.1 years ago by ▴ 250 • written 12.2 years ago by 16k
0
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0
replies
950
views
help with forging a BSgenome data
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
12.2 years ago Hervé Pagès 16k
0
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0
replies
753
views
Finding Candidate Binding Sites for multiple Known Transcription Factors simultaneously
Cancer Cancer
12.2 years ago Hervé Pagès 16k
0
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0
replies
1.7k
views
fdr cutoff
Cancer Cancer
12.2 years ago Richard Friedman ★ 2.0k
0
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2
replies
1.5k
views
Fwd: BioStrings PairwiseAlignment deletion() insertion() function
Alignment Cancer Biostrings IRanges Alignment Cancer Biostrings IRanges
updated 12.2 years ago by ▴ 30 • written 12.2 years ago by 16k
0
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0
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1.7k
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Bioinformatics Position in Oncology / Multiple Myeloma, Univ. Heidelberg
Sequencing Cancer Sequencing Cancer
12.2 years ago Wolfgang Huber ★ 13k
0
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2
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1.4k
views
Unusual results with DESeq ?
miRNA Cancer DESeq miRNA Cancer DESeq
updated 12.2 years ago by ★ 3.8k • written 12.2 years ago by ▴ 40
0
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1
reply
1.6k
views
Question about Diffbind input control
Cancer DESeq DiffBind Cancer DESeq DiffBind
12.2 years ago Rory Stark ★ 5.2k
0
votes
2
replies
1.7k
views
Affymetrix HTA 2 array analysis
Cancer Breast Cancer Breast
updated 12.2 years ago by 6.7k • written 12.2 years ago by ▴ 910
0
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0
replies
2.7k
views
8. CGHCall problems (Bernard North [guest]) : Bioconductor Digest, Vol 126, Issue 7
aCGH RNASeq ChIPSeq Proteomics Annotation Normalization GO Network Cancer ChipName probe
12.2 years ago Sarah JugurnauthLittle ▴ 20
0
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1
reply
1.0k
views
[devteam-bioc] Depth of Coverage and Base counts from BAM file
Coverage Cancer Rsamtools Coverage Cancer Rsamtools
12.2 years ago Hervé Pagès 16k
0
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0
replies
3.3k
views
DiffBind questions
Transcription Cancer DiffBind MMDiff Transcription Cancer DiffBind MMDiff
12.3 years ago Rory Stark ★ 5.2k
0
votes
0
replies
2.5k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria
Alignment Annotation Normalization GO Preprocessing Clustering Cancer Organism probe GLAD
12.3 years ago Sarah Pohl ▴ 30
0
votes
0
replies
861
views
Course: Understanding R / Bioconductor, Sept 30-Oct 1, Seattle
Cancer Biostrings biomaRt IRanges GenomicRanges Cancer Biostrings biomaRt IRanges
12.3 years ago Martin Morgan 25k
0
votes
1
reply
2.6k
views
Semantics of GenomicRanges gaps()
Cancer GenomicRanges trigger Cancer GenomicRanges trigger
updated 12.3 years ago by ★ 6.8k • written 12.3 years ago by ▴ 210
0
votes
0
replies
736
views
FW: Computational biology position
Cancer Cancer
12.3 years ago Zhang,Jianhua ▴ 10
0
votes
0
replies
972
views
Bioconductor Job Opportunities
Annotation Cancer Annotation Cancer
12.3 years ago Martin Morgan 25k
0
votes
0
replies
821
views
HTqPCR package
Normalization Cancer Normalization Cancer
12.3 years ago VETTER Guillaume ▴ 10
0
votes
2
replies
1.2k
views
DNAStringSetList can't coerce a list?
Cancer Cancer
12.3 years ago Taylor, Sean D ▴ 250
0
votes
8
replies
2.2k
views
Filtering BAM files by start position for VariantTools
Coverage Cancer cycle VariantTools Coverage Cancer cycle VariantTools
updated 12.3 years ago by ▴ 250 • written 12.3 years ago by 25k
0
votes
0
replies
805
views
rtracklayer problem on large number of GRanges
Cancer Cancer
12.3 years ago Janet Young ▴ 740
1,555 results • Page 5 of 32
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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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