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News: Hands-on Bioconductor course, 7 Sept 2015, Tokyo
sequencing transcription variantfiltering annotation News
8.9 years ago Matthew Ritchie ▴ 1000
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News: BioCAsia, 8 Sept 2015, Tokyo
sequencing transcription epigenomics visualization infrastructure News
8.9 years ago • updated 8.7 years ago Matthew Ritchie ▴ 1000
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question on MotifDb package
Transcription MotifDb Transcription MotifDb
10.2 years ago Paul Shannon ▴ 470
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924
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Bioconductor for predicting transcription factors from a gene list?
transcription transcriptdb
7.0 years ago hkarakurt ▴ 20
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4
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Is GO.db out of date?
Transcription GO Transcription GO
11.1 years ago chawla ▴ 190
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News: BioCAsia, 4th November 2016, Brisbane, Australia
conference transcription epigenomics visualization infrastructure News
7.8 years ago Matthew Ritchie ▴ 1000
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biomart Ensembl Regulatory Build
SNP Transcription biomaRt SNP Transcription biomaRt
13.0 years ago Fabrice Tourre ▴ 970
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DESeq2: Tests of log2 differences
deseq2 rna-seq transcription dgea
6.9 years ago fabian ▴ 40
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5
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2.2k
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paCalls oligo package
Transcription oligo Transcription oligo
updated 11.6 years ago by 65k • written 11.6 years ago by ▴ 190
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clustering of genes
Transcription Clustering Cancer Transcription Clustering Cancer
updated 21.0 years ago by ★ 13k • written 21.0 years ago by 50k
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retrieving genomic sequences with biomaRt
Transcription biomaRt Transcription biomaRt
updated 17.6 years ago by ▴ 580 • written 17.6 years ago by ★ 1.9k
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annotation - 1 probe with 2 UG ??
Transcription Annotation GO hgu133a probe Transcription Annotation GO hgu133a probe
updated 19.7 years ago by ★ 2.9k • written 19.7 years ago by ▴ 300
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Gramene now available via biomaRt
SNP Transcription biomaRt Vega SNP Transcription biomaRt Vega
updated 7.5 years ago by • 0 • written 17.2 years ago by ▴ 580
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2
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Transcription factor binding site information
Transcription Transcription
17.0 years ago Ольга Камнева ▴ 90
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An. Gambie RNA-Seq differential expression using gage and pathview
Transcription Annotation Normalization gage pathview Transcription Annotation Normalization
updated 9.8 years ago by ▴ 20 • written 9.8 years ago by ★ 1.6k
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Differential expression analysis of CAGE data
Transcription Annotation convert edgeR DESeq Transcription Annotation convert edgeR DESeq
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ▴ 30
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Q1, efficiency of experimental designs
Transcription Transcription
19.7 years ago Michael Gates ▴ 40
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2
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Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 8.8 years ago by • 0 • written 11.1 years ago by ★ 8.2k
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BSgenomes vs ENSEMBL
Transcription Annotation BSgenome annotate Biostrings BSgenome Transcription Annotation
updated 15.6 years ago by 16k • written 15.6 years ago by ★ 3.9k
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normalization
Transcription Microarray Transcription Microarray
updated 19.9 years ago by ▴ 920 • written 19.9 years ago by ▴ 90
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TilingArray Normalization
Transcription Normalization probe tilingArray Transcription Normalization probe tilingArray
updated 15.4 years ago by ★ 13k • written 15.4 years ago by ▴ 90
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How to retrieve 'conservation score' sequence?
Transcription biomaRt Transcription biomaRt
updated 15.4 years ago by ▴ 620 • written 15.4 years ago by ★ 3.9k
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synergy / interaction analysis between gene transcript & correlation / what package to do this ?
Transcription Transcription
15.3 years ago Philippe Guardiola ▴ 10
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interaction analysis
Transcription Transcription
15.3 years ago Phguardiol@aol.com ▴ 720
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GSEA to discover co-regulated genes
Transcription Pathways Transcription Pathways
updated 15.3 years ago by 6.7k • written 15.3 years ago by ★ 1.3k
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Using ChIPpeakAnno on a non-mainstream organism
Transcription Annotation GO AnnotationData Organism BSgenome biomaRt BSgenome ChIPpeakAnno
13.0 years ago Julie Zhu ★ 4.3k
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GSEA to discover co-regulated genes
Transcription Annotation Pathways Infrastructure probe convert GSEABase Transcription
15.3 years ago Paul Geeleher ★ 1.3k
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interaction analysis
Transcription Microarray Network qpgraph Transcription Microarray Network qpgraph
15.2 years ago Robert Castelo ★ 3.3k
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979
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Finding transcription factors controlling hk1 gene In timecourse experiment
Transcription TimeCourse affy timecourse Transcription TimeCourse affy timecourse
updated 15.0 years ago by ▴ 110 • written 15.0 years ago by ▴ 10
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PWM matching using matchPWM in Biostrings
Transcription BSgenome Biostrings BSgenome Transcription BSgenome Biostrings BSgenome
updated 15.0 years ago by ★ 1.6k • written 15.0 years ago by ▴ 10
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Low number of replicates DESeq
Transcription GO DESeq2 Transcription GO DESeq2
updated 10.2 years ago by 41k • written 10.2 years ago by ▴ 130
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matching transcription factor binding sites
Transcription Transcription
updated 16.1 years ago by 16k • written 16.1 years ago by ▴ 330
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R: How can I trace back transcription target genes from the miRNAs file downloadable from miRbase ?
Transcription miRNA Homo sapiens biomaRt Transcription miRNA Homo sapiens biomaRt
updated 14.6 years ago by ▴ 580 • written 14.6 years ago by ▴ 870
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1
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604
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How can I trace back transcription target genes from the miRNAs file downloadable from miRbase ?
Transcription miRNA Transcription miRNA
updated 14.6 years ago by 21k • written 14.6 years ago by ▴ 870
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gDNA Cy3, cDNA Cy5
Transcription Biobase annotate Transcription Biobase annotate
updated 16.6 years ago by ★ 13k • written 16.6 years ago by ▴ 270
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5
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Problem reading in files with marrayInput
Transcription Cancer Transcription Cancer
updated 20.5 years ago by 65k • written 20.5 years ago by ★ 2.0k
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R: R: How can I trace back transcription target genes from the miRNAs file downloadable from miRbase ?
Transcription miRNA Cancer Homo sapiens biomaRt microRNA Transcription miRNA Cancer
14.6 years ago mauede@alice.it ▴ 870
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General Transcription USD 0.42
Transcription Transcription
14.6 years ago prakashpatodia@cabbagetreesolutions.com ▴ 10
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1.0k
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question about ontoCompare() performance change
Transcription GO hgu133a goTools Transcription GO hgu133a goTools
updated 14.5 years ago by ★ 7.4k • written 14.5 years ago by ▴ 50
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Help with Oligo Package: Extracting and Graphing
Transcription Normalization Yeast probe affy graph tilingArray oligo pdInfoBuilder Starr
updated 14.5 years ago by ▴ 430 • written 14.5 years ago by ▴ 410
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exon and transcription start site locations
Transcription GO Transcription GO
updated 14.4 years ago by ▴ 620 • written 14.4 years ago by ▴ 180
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1
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979
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TSS Regions
Transcription IRanges Transcription IRanges
updated 14.4 years ago by ★ 4.3k • written 14.4 years ago by ▴ 130
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993
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Limma- deleting control probes from differential expression analysis
Transcription ASSIGN Transcription ASSIGN
14.4 years ago Neel Aluru ▴ 460
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5
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1.4k
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from TF DNA binding motif to downstream genes?
Transcription Biostrings Transcription Biostrings
updated 14.3 years ago by ★ 1.6k • written 14.3 years ago by ★ 1.1k
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ChIPpeakAnno
Transcription ChIPpeakAnno Transcription ChIPpeakAnno
14.3 years ago • updated 14.2 years ago Julie Zhu ★ 4.3k
0
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1
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973
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concurrent R-release & R-devel versions -- bioc also? [was Re: from TF DNA binding motif to downstream genes?]
Transcription GO celegans BSgenome Biostrings BSgenome IRanges Transcription GO celegans
updated 14.2 years ago by 21k • written 14.2 years ago by ★ 1.1k
0
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2
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1.4k
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chip-seq data analysis
Transcription ChIPSeq Alignment chipseq Transcription ChIPSeq Alignment chipseq
updated 14.2 years ago by 21k • written 14.2 years ago by ▴ 60
0
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2
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1.1k
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simple functional analysis of gene lists
Transcription GO convert Transcription GO convert
updated 14.1 years ago by ▴ 190 • written 14.1 years ago by ▴ 60
0
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0
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921
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ChIPpeakAnno Paper - Example Dataset not found
Transcription ChIPSeq Annotation chipseq genomes Transcription ChIPSeq Annotation chipseq
13.9 years ago Julie Zhu ★ 4.3k
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0
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Job advertisement
Transcription Sequencing Microarray Normalization Pathways PROcess Transcription Sequencing
14.6 years ago Alexandre Kuhn ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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