Showing : transcription • reset
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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
3
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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
1
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question on MotifDb package
Transcription MotifDb Transcription MotifDb
10.2 years ago Paul Shannon ▴ 470
1
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0
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926
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Bioconductor for predicting transcription factors from a gene list?
transcription transcriptdb
7.0 years ago hkarakurt ▴ 20
1
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4
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1.5k
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Is GO.db out of date?
Transcription GO Transcription GO
11.2 years ago • updated 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
1
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0
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1.1k
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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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4
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1.2k
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DESeq2: Tests of log2 differences
deseq2 rna-seq transcription dgea
7.0 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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2
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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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3
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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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1
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855
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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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3
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2.3k
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Gramene now available via biomaRt
SNP Transcription biomaRt Vega SNP Transcription biomaRt Vega
updated 7.6 years ago by • 0 • written 17.2 years ago by ▴ 580
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2
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949
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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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678
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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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3.8k
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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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4
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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 20.0 years ago by ▴ 920 • written 20.0 years ago by ▴ 90
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901
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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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721
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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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1.0k
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interaction analysis
Transcription Transcription
15.3 years ago Phguardiol@aol.com ▴ 720
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1
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1.0k
views
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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1.2k
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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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1
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980
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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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2
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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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7
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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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3
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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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3
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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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605
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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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2
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1.0k
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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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728
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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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1
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1.2k
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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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1.5k
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exon and transcription start site locations
Transcription GO Transcription GO
updated 14.5 years ago by ▴ 620 • written 14.5 years ago by ▴ 180
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1
reply
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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994
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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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974
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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 14.3 years ago by 21k • written 14.3 years ago by ★ 1.1k
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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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923
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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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1.2k
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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 ...
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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