Showing : transcription • reset
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Is there a Bioconductor package to calculate TFs regulatory networks?
TFs Transcription regulator
3.2 years ago OliverBoynton • 0
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2.3k
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Getting annotation into GOstat
Transcription Transcription
updated 7.6 years ago by • 0 • written 12.9 years ago by ★ 6.0k
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Reference annotation file contains only transcript and CDS information, how to analyze the different expression of genes?
transcription hisat2
7.8 years ago zoukai3412085 • 0
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Job: PhD computational position - Milan
epigenetics transcription computational biology Job
8.2 years ago mattia pelizzola ▴ 200
1
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4
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1.6k
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DESeq2: Tests of log2 differences
deseq2 rna-seq transcription dgea
8.3 years ago fabian ▴ 40
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Bioconductor for predicting transcription factors from a gene list?
transcription transcriptdb
8.3 years ago hkarakurt ▴ 20
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1
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1.9k
views
TF ANALYSIS USING JASPAR
transcription jaspar
updated 8.4 years ago by 68k • written 8.4 years ago by ▴ 30
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3
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2.8k
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Gramene now available via biomaRt
SNP Transcription biomaRt Vega SNP Transcription biomaRt Vega
updated 8.9 years ago by • 0 • written 18.6 years ago by ▴ 580
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News: BioCAsia, 4th November 2016, Brisbane, Australia
conference transcription epigenomics visualization infrastructure News
9.2 years ago Matthew Ritchie ▴ 1000
3
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News: BioCAsia, 8 Sept 2015, Tokyo
sequencing transcription epigenomics visualization infrastructure News
10.2 years ago • updated 10.1 years ago Matthew Ritchie ▴ 1000
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2
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4.3k
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Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 10.2 years ago by • 0 • written 12.5 years ago by ★ 8.2k
4
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0
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1.8k
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News: Hands-on Bioconductor course, 7 Sept 2015, Tokyo
sequencing transcription variantfiltering annotation News
10.2 years ago Matthew Ritchie ▴ 1000
0
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1
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2.8k
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Interspecies differential expression of orthologs with Edger
Transcription edgeR Transcription edgeR
11.1 years ago Tim Triche ★ 4.2k
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11
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2.7k
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Interspecies differential expression of orthologs with Edger
Transcription edgeR Transcription edgeR
updated 11.1 years ago by 53k • written 11.1 years ago by ▴ 140
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rsqlite for windows from fhcrc
Transcription BiocInstaller Transcription BiocInstaller
updated 11.1 years ago by 25k • written 11.1 years ago by ★ 6.5k
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1.5k
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Useful information about Ensembl release 76 mart databases
Transcription zebrafish Transcription zebrafish
11.1 years ago Thomas Maurel ▴ 800
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1
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2.0k
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An. Gambie RNA-Seq differential expression using gage and pathview
Transcription Annotation Normalization gage pathview Transcription Annotation Normalization
updated 11.2 years ago by ▴ 20 • written 11.2 years ago by ★ 1.6k
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An. Gambie RNA-Seq differential expression using gage and pathview
Transcription Normalization gage Transcription Normalization gage
11.2 years ago Saul Lozano ▴ 20
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4
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1.8k
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Limma package and minimal number of genes
Transcription limma Transcription limma
updated 11.3 years ago by ★ 1.3k • written 11.3 years ago by ▴ 10
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1.4k
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total count filter cutoff
Transcription Transcription
updated 11.4 years ago by ▴ 20 • written 11.4 years ago by ★ 13k
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1
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2.5k
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Deseq2-help
Transcription DESeq DESeq2 Transcription DESeq DESeq2
updated 11.5 years ago by ▴ 30 • written 11.4 years ago by 43k
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question on MotifDb package
Transcription MotifDb Transcription MotifDb
11.5 years ago Paul Shannon ▴ 470
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7
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2.6k
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Low number of replicates DESeq
Transcription GO DESeq2 Transcription GO DESeq2
updated 11.5 years ago by 43k • written 11.5 years ago by ▴ 130
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0
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1.7k
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questions related to DiffBind package
Transcription Normalization DiffBind Transcription Normalization DiffBind
11.6 years ago Rory Stark ★ 5.2k
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1
reply
1.8k
views
DiffBind loading Problem
Transcription ChIPSeq chipseq DiffBind Transcription ChIPSeq chipseq DiffBind
11.6 years ago Rory Stark ★ 5.2k
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4
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1.9k
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Rcade analysis without ChIP-seq replicates
Transcription Rcade Transcription Rcade
updated 11.6 years ago by ▴ 60 • written 11.6 years ago by ▴ 30
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2
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2.6k
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ensemblVEP, variant_effect_predictor versions and release schedule
Transcription HapMap PolyPhen SIFT convert genomes ensemblVEP Transcription HapMap SIFT
updated 11.7 years ago by ★ 6.8k • written 11.7 years ago by ▴ 30
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1
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2.3k
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Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription Annotation Normalization GO hgu133plus2 affy PROcess Category Transcription
updated 11.8 years ago by ▴ 80 • written 11.8 years ago by ▴ 20
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4.6k
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Bioconductor 2.13 is released
BiocViews aCGH SNP Transcription Sequencing miRNA Microarray Genetics Proteomics Coverage
11.9 years ago Dan Tenenbaum ★ 8.2k
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1.5k
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DNaseR - a new Bioconductor package for DNase-seq digital genomic footprinting
Transcription DNaseR Transcription DNaseR
11.9 years ago Pedro Madrigal ▴ 20
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3.3k
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DiffBind questions
Transcription Cancer DiffBind MMDiff Transcription Cancer DiffBind MMDiff
12.1 years ago Rory Stark ★ 5.2k
0
votes
2
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4.4k
views
TranscriptDb of GENCODE Genes
Transcription Annotation Transcription Annotation
updated 12.1 years ago by ★ 7.2k • written 12.1 years ago by ★ 1.6k
1
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4
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1.9k
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Is GO.db out of date?
Transcription GO Transcription GO
12.5 years ago chawla ▴ 190
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2
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1.5k
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matchPWM() questions
Transcription Transcription
updated 12.5 years ago by 16k • written 12.5 years ago by ▴ 340
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1.3k
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BitSeq: Required input for 3' bias correction on transcripts.
Transcription RNASeq safe BitSeq Transcription RNASeq safe BitSeq
12.6 years ago Peter Glaus ▴ 70
0
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1
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2.0k
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promoter prediction
Transcription MotIV MotifDb Transcription MotIV MotifDb
updated 12.8 years ago by ▴ 380 • written 12.8 years ago by ▴ 750
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ComBat
Transcription Genetics Pathways Network Survival Cancer Breast Colon Kidney Leukemia HIV
12.9 years ago SSc Array Core ▴ 10
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3.5k
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Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
13.0 years ago Dan Tenenbaum ★ 8.2k
1
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5
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2.6k
views
paCalls oligo package
Transcription oligo Transcription oligo
updated 13.0 years ago by 68k • written 13.0 years ago by ▴ 190
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1
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2.1k
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Bioconductor Digest, Vol 115, Issue 22
Transcription Sequencing miRNA SmallRNA Annotation Normalization GO Cancer Organism edgeR
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 10
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1.5k
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NGS public data analysis
Transcription DEGseq Transcription DEGseq
13.0 years ago Jill Pleasance ▴ 10
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1
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1.7k
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Differential expression analysis of CAGE data
Transcription Annotation convert edgeR DESeq Transcription Annotation convert edgeR DESeq
updated 13.0 years ago by ★ 13k • written 13.0 years ago by ▴ 30
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1.2k
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ChIPpeakAnno - c elegans annotation feature type: translation start site
Transcription Transcription
13.1 years ago Julie Zhu ★ 4.3k
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4
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5.3k
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GRanges DitancetoNearest query
Transcription GenomicRanges Transcription GenomicRanges
updated 13.1 years ago by ★ 13k • written 13.1 years ago by ▴ 150
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0
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1.2k
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GOstats adding custom annotations
Transcription miRNA GO Transcription miRNA GO
13.2 years ago sudeep s ▴ 60
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2
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2.1k
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goTools: Error in goidvect[test] : invalid subscript type \'list\'
Transcription Microarray Annotation GO goTools Transcription Microarray Annotation GO
updated 13.2 years ago by 68k • written 13.2 years ago by ★ 13k
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4
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1.8k
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AffyID mapping question
Transcription mouse4302 Transcription mouse4302
updated 13.2 years ago by ★ 7.2k • written 13.2 years ago by ★ 13k
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11
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3.3k
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"graphite" Biocarta 'native' graphs different from Biocarta web site?
Transcription Pathways Leukemia graphite Transcription Pathways Leukemia graphite
13.3 years ago Hamid Bolouri ▴ 90
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5
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2.0k
views
predicting transcription factors
Transcription Transcription
updated 13.3 years ago by ▴ 750 • written 13.3 years ago by ▴ 380
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1
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1.5k
views
Biological Pathway Database
Transcription Pathways Category Transcription Pathways Category
written 13.4 years ago by ▴ 10
113 results • Page 1 of 3
Recent ...
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Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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