Showing : Cancer • reset
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pca plot
Cancer Cancer
11.4 years ago Guest User ★ 13k
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DESeq2: detect significantly increasing across an ordinal variable
RNASeq Cancer DESeq2 RNASeq Cancer DESeq2
updated 11.4 years ago by 43k • written 11.4 years ago by ▴ 100
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[Bioc-devel] granges() method for GenomicRanges objects akin to ranges()...
Cancer GenomicRanges Cancer GenomicRanges
updated 11.4 years ago by ★ 1.3k • written 11.4 years ago by 16k
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SomaticSignatures
Annotation Cancer convert Annotation Cancer convert
updated 11.4 years ago by ★ 1.3k • written 11.4 years ago by ▴ 90
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GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 11.4 years ago by ▴ 320 • written 11.4 years ago by ★ 6.8k
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Quickly approaching: BioC 2014, Boston, July 31 - Aug 1
Cancer Cancer
11.4 years ago Martin Morgan 25k
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1.6k
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Thread safety of BSgenome getSeq()
Cancer BSgenome PROcess BSgenome Rsamtools Cancer BSgenome PROcess BSgenome Rsamtools
updated 11.4 years ago by 16k • written 11.4 years ago by ▴ 90
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Bioconductor newsletter - July 2014
Cancer Cancer
11.4 years ago Valerie Obenchain ★ 6.8k
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segfault in rqubic
Microarray Cancer rqubic Microarray Cancer rqubic
11.4 years ago Zhang, Jitao David ▴ 120
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1.8k
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OpenCyto
Cancer eisa openCyto Cancer eisa openCyto
11.5 years ago • updated 11.4 years ago Jiang, Mike ★ 1.3k
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singe_sequences.fa.gz file in Bsgenome.Hsapiens.NCBI.GRCh38 is too big
Cancer BSgenome BSgenome Cancer BSgenome BSgenome
11.5 years ago Hervé Pagès 16k
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1.3k
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Possible problem with featureCounts() and scipen
Annotation Cancer Breast Rsubread Annotation Cancer Breast Rsubread
updated 11.5 years ago by ★ 3.6k • written 11.5 years ago by ▴ 10
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2.2k
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Creating DataFrame uses too much memory
Cancer PROcess Cancer PROcess
updated 11.5 years ago by ★ 11k • written 11.5 years ago by ▴ 40
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crlmm of other software for oncoscan
Cancer crlmm Cancer crlmm
11.5 years ago Richard Friedman ▴ 80
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3
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1.3k
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DESeq analysis of resistance data
RNASeq Cancer DESeq2 RNASeq Cancer DESeq2
updated 11.5 years ago by 43k • written 11.5 years ago by ★ 13k
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858
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BioC2014 travel scholarship deadline June 10
Cancer Cancer
11.5 years ago Martin Morgan 25k
0
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2
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1.3k
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VCF class: different length when unlisting INFO CompressedCharacterList
Cancer Cancer
updated 11.5 years ago by ★ 11k • written 11.5 years ago by ▴ 50
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4
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1.9k
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GenomicAlignments and QNAME collision
RNASeq Cancer convert Rsamtools GenomicAlignments RNASeq Cancer convert Rsamtools
updated 11.5 years ago by ▴ 90 • written 11.5 years ago by ★ 6.8k
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HTqPCR bug in geometric mean normalization
Normalization Cancer Normalization Cancer
11.5 years ago Johannes Rainer ▴ 80
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909
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Bioc 2014: reduced hotel rates
Cancer Cancer
11.5 years ago Martin Morgan 25k
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2
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2.6k
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UCSC data anomaly in 50638 transcript(s): the cds cumulative length is
Genetics GO Regression Cancer TranscriptDb Genetics GO Regression Cancer TranscriptDb
updated 11.5 years ago by ▴ 570 • written 11.5 years ago by 16k
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VCF class: different length when unlisting INFO CompressedCharacterList
Cancer Cancer
updated 11.5 years ago by ★ 11k • written 11.5 years ago by ▴ 50
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0
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1.0k
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[devteam-bioc] readGAlignmentPairs perfromace issue
RNASeq Cancer RNASeq Cancer
11.5 years ago Hervé Pagès 16k
0
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5
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1.6k
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information retrieval from pubmed
Cancer Cancer
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ▴ 230
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2
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1.7k
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Fwd: adjusted P-values
Cancer genefilter Cancer genefilter
updated 11.6 years ago by ★ 4.2k • written 11.6 years ago by ▴ 190
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983
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BioC 2014 Registration Open
Cancer Cancer
11.6 years ago Martin Morgan 25k
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1.8k
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SomaticSignatures
Cancer BiocParallel Cancer BiocParallel
11.6 years ago Martin Morgan 25k
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2.5k
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Affymetrix HTA 2 array analysis
BiocViews Annotation Cancer Breast Organism PROcess biocViews pdInfoBuilder BiocViews
11.6 years ago Elena Serrano ▴ 30
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1
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2.0k
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TCC::ERROR: Need the design matrix for GLM
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 11.6 years ago by ▴ 10 • written 11.6 years ago by 53k
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TCC::ERROR: Need the design matrix for GLM.
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 11.6 years ago by ▴ 10 • written 11.6 years ago by ▴ 100
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lumi - limma contrast design
Cancer Cancer
updated 11.6 years ago by ★ 1.1k • written 11.6 years ago by ▴ 350
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2.9k
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SomaticSignatures
Cancer SomaticSignatures Cancer SomaticSignatures
updated 11.6 years ago by ★ 1.3k • written 11.7 years ago by ★ 8.2k
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2.4k
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It works! RE: So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer
updated 11.6 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
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1.5k
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RangedData change space information
Cancer TEQC Cancer TEQC
updated 11.6 years ago by ★ 11k • written 11.6 years ago by ▴ 240
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Trying to use BSgenome.Hsapiens.NCBI.GRCh38
Cancer BSgenome BSgenome genomes Cancer BSgenome BSgenome genomes
11.7 years ago Hervé Pagès 16k
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5
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2.2k
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A question about the function readGAlignmentPairs in GenomicRnages package
Alignment Cancer convert GenomicAlignments Alignment Cancer convert GenomicAlignments
updated 11.7 years ago by 16k • written 11.7 years ago by ▴ 50
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1.0k
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justRMA (package Affy) messing up phenoData when passing an AnnotatedDataFrame
Annotation Cancer Annotation Cancer
updated 11.7 years ago by 68k • written 11.7 years ago by ▴ 100
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So close, but still error: RE: Rsamtools filtering bam file: RE: MEDIPS.createSet error
Alignment GO Cancer BSgenome BSgenome Rsamtools genomes MEDIPS Alignment GO Cancer
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ▴ 220
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1.8k
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Job: PhD and postdoc position at DKFZ Heidelberg
Cancer Cancer
11.7 years ago Bernd Fischer ▴ 550
0
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2
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894
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Bioconductor newsletter: April 2014
Cancer Cancer
updated 11.7 years ago by ★ 1.6k • written 11.7 years ago by ★ 6.8k
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3
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2.7k
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views on Rle using GRanges object
RNASeq Coverage GO Cancer bridge rtracklayer IRanges RNASeq Coverage GO Cancer bridge
updated 11.7 years ago by 16k • written 11.7 years ago by ★ 11k
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5
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1.7k
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A question about the function readGAlignmentPairs in GenomicRnages package
Cancer Cancer
11.7 years ago Hervé Pagès 16k
0
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5
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3.9k
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overlap regions between two GRanges (or GRangesList)
Cancer Cancer
updated 11.7 years ago by ▴ 20 • written 11.7 years ago by 16k
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1.3k
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Conference Announcement - CAMDA 2014
Genetics Cancer Genetics Cancer
11.7 years ago Djork Clevert ▴ 210
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2.7k
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WGCNA RNAseq
RNASeq Cancer trigger RNASeq Cancer trigger
11.8 years ago Anna Esteve Codina ▴ 20
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2
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2.2k
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subsetting SummarizedExperiments - a proposal (or a hack?)
Cancer IRanges GenomicRanges PROMISE Cancer IRanges GenomicRanges PROMISE
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ★ 1.6k
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1
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2.2k
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edgeR, multifactorial design
RNASeq Cancer edgeR RNASeq Cancer edgeR
updated 11.8 years ago by 53k • written 11.8 years ago by ▴ 70
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2
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1.2k
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cluster or pattern analysis of expression and CN data of cell lines
Cancer Cancer
updated 11.8 years ago by ★ 4.2k • written 11.8 years ago by ▴ 20
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0
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1.2k
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Seattle Short Course, Feb 27-28: Introduction to Bioconductor for Sequence Analysis
RNASeq Visualization Cancer RNASeq Visualization Cancer
11.8 years ago Martin Morgan 25k
0
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9
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2.6k
views
variantAnnotation: alternative GENETIC_CODE, and circular chromosomes?
VariantAnnotation Cancer Yeast annotate Biostrings VariantAnnotation VariantAnnotation
updated 11.8 years ago by 16k • written 11.8 years ago by ▴ 740
1,555 results • Page 4 of 32
Recent ...
Replies
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.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
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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