Showing : Transcription • reset
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Is there a Bioconductor package to calculate TFs regulatory networks?
TFs Transcription regulator
7 weeks ago OliverBoynton • 0
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2
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1.5k
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Getting annotation into GOstat
Transcription Transcription
updated 4.5 years ago by • 0 • written 9.8 years ago by ★ 6.0k
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1
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654
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Reference annotation file contains only transcript and CDS information, how to analyze the different expression of genes?
transcription hisat2
4.7 years ago zoukai3412085 • 0
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0
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715
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Job: PhD computational position - Milan
epigenetics transcription computational biology Job
5.1 years ago mattia pelizzola ▴ 200
1
vote
4
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820
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DESeq2: Tests of log2 differences
deseq2 rna-seq transcription dgea
5.2 years ago fabian ▴ 40
1
vote
0
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669
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Bioconductor for predicting transcription factors from a gene list?
transcription transcriptdb
5.3 years ago hkarakurt ▴ 20
0
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1
reply
849
views
TF ANALYSIS USING JASPAR
transcription jaspar
updated 5.3 years ago by 60k • written 5.3 years ago by ▴ 30
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3
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1.7k
views
Gramene now available via biomaRt
SNP Transcription biomaRt Vega SNP Transcription biomaRt Vega
updated 5.8 years ago by • 0 • written 15.5 years ago by ▴ 580
1
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1.0k
views
News: BioCAsia, 4th November 2016, Brisbane, Australia
conference transcription epigenomics visualization infrastructure News
6.1 years ago Matthew Ritchie ▴ 1000
3
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0
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1.2k
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News: BioCAsia, 8 Sept 2015, Tokyo
sequencing transcription epigenomics visualization infrastructure News
7.2 years ago • updated 7.0 years ago Matthew Ritchie ▴ 1000
0
votes
2
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3.0k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 7.1 years ago by • 0 • written 9.4 years ago by ★ 8.2k
4
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0
replies
1.1k
views
News: Hands-on Bioconductor course, 7 Sept 2015, Tokyo
sequencing transcription variantfiltering annotation News
7.2 years ago Matthew Ritchie ▴ 1000
0
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1
reply
2.1k
views
Interspecies differential expression of orthologs with Edger
Transcription edgeR Transcription edgeR
8.0 years ago Tim Triche ★ 4.2k
0
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11
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1.3k
views
Interspecies differential expression of orthologs with Edger
Transcription edgeR Transcription edgeR
updated 8.0 years ago by 46k • written 8.0 years ago by ▴ 140
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1
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1.0k
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rsqlite for windows from fhcrc
Transcription BiocInstaller Transcription BiocInstaller
updated 8.0 years ago by 25k • written 8.0 years ago by 6.5k
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0
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900
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Useful information about Ensembl release 76 mart databases
Transcription zebrafish Transcription zebrafish
8.0 years ago Thomas Maurel ▴ 790
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1
reply
1.3k
views
An. Gambie RNA-Seq differential expression using gage and pathview
Transcription Annotation Normalization gage pathview Transcription Annotation Normalization
updated 8.1 years ago by ▴ 20 • written 8.1 years ago by ★ 1.5k
0
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0
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884
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An. Gambie RNA-Seq differential expression using gage and pathview
Transcription Normalization gage Transcription Normalization gage
8.1 years ago Saul Lozano ▴ 20
0
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4
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933
views
Limma package and minimal number of genes
Transcription limma Transcription limma
updated 8.2 years ago by ★ 1.3k • written 8.2 years ago by ▴ 10
0
votes
1
reply
893
views
total count filter cutoff
Transcription Transcription
updated 8.3 years ago by ▴ 20 • written 8.3 years ago by 13k
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1
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1.8k
views
Deseq2-help
Transcription DESeq DESeq2 Transcription DESeq DESeq2
updated 8.4 years ago by ▴ 30 • written 8.4 years ago by 37k
1
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1.0k
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question on MotifDb package
Transcription MotifDb Transcription MotifDb
8.4 years ago Paul Shannon ▴ 470
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7
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1.6k
views
Low number of replicates DESeq
Transcription GO DESeq2 Transcription GO DESeq2
updated 8.5 years ago by 37k • written 8.5 years ago by ▴ 130
0
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0
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1.0k
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questions related to DiffBind package
Transcription Normalization DiffBind Transcription Normalization DiffBind
8.5 years ago Rory Stark ★ 4.4k
0
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1
reply
1.2k
views
DiffBind loading Problem
Transcription ChIPSeq chipseq DiffBind Transcription ChIPSeq chipseq DiffBind
8.5 years ago Rory Stark ★ 4.4k
0
votes
4
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1.1k
views
Rcade analysis without ChIP-seq replicates
Transcription Rcade Transcription Rcade
updated 8.5 years ago by ▴ 60 • written 8.5 years ago by ▴ 30
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2
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1.6k
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ensemblVEP, variant_effect_predictor versions and release schedule
Transcription HapMap PolyPhen SIFT convert genomes ensemblVEP Transcription HapMap SIFT
updated 8.6 years ago by ★ 6.7k • written 8.6 years ago by ▴ 30
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1
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1.5k
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Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription Annotation Normalization GO hgu133plus2 affy PROcess Category Transcription
updated 8.7 years ago by ▴ 80 • written 8.7 years ago by ▴ 20
0
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0
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3.4k
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Bioconductor 2.13 is released
BiocViews aCGH SNP Transcription Sequencing miRNA Microarray Genetics Proteomics Coverage
8.8 years ago Dan Tenenbaum ★ 8.2k
0
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0
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998
views
DNaseR - a new Bioconductor package for DNase-seq digital genomic footprinting
Transcription DNaseR Transcription DNaseR
8.8 years ago Pedro Madrigal ▴ 20
0
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0
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2.6k
views
DiffBind questions
Transcription Cancer DiffBind MMDiff Transcription Cancer DiffBind MMDiff
9.0 years ago Rory Stark ★ 4.4k
0
votes
2
replies
3.0k
views
TranscriptDb of GENCODE Genes
Transcription Annotation Transcription Annotation
updated 9.0 years ago by ★ 7.2k • written 9.0 years ago by ★ 1.5k
1
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4
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1.1k
views
Is GO.db out of date?
Transcription GO Transcription GO
9.4 years ago chawla ▴ 190
0
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2
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873
views
matchPWM() questions
Transcription Transcription
updated 9.4 years ago by 15k • written 9.4 years ago by ▴ 340
0
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0
replies
779
views
BitSeq: Required input for 3' bias correction on transcripts.
Transcription RNASeq safe BitSeq Transcription RNASeq safe BitSeq
9.5 years ago Peter Glaus ▴ 70
0
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1
reply
1.3k
views
promoter prediction
Transcription MotIV MotifDb Transcription MotIV MotifDb
updated 9.7 years ago by ▴ 380 • written 9.7 years ago by ▴ 750
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0
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2.7k
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ComBat
Transcription Genetics Pathways Network Survival Cancer Breast Colon Kidney Leukemia HIV
9.8 years ago SSc Array Core ▴ 10
0
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0
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2.6k
views
Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
9.9 years ago Dan Tenenbaum ★ 8.2k
1
vote
5
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1.8k
views
paCalls oligo package
Transcription oligo Transcription oligo
updated 9.9 years ago by 60k • written 9.9 years ago by ▴ 190
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1
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1.3k
views
Bioconductor Digest, Vol 115, Issue 22
Transcription Sequencing miRNA SmallRNA Annotation Normalization GO Cancer Organism edgeR
updated 9.9 years ago by 13k • written 9.9 years ago by ▴ 10
0
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0
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935
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NGS public data analysis
Transcription DEGseq Transcription DEGseq
9.9 years ago Jill Pleasance ▴ 10
0
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1
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1.2k
views
Differential expression analysis of CAGE data
Transcription Annotation convert edgeR DESeq Transcription Annotation convert edgeR DESeq
updated 9.9 years ago by 13k • written 9.9 years ago by ▴ 30
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0
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637
views
ChIPpeakAnno - c elegans annotation feature type: translation start site
Transcription Transcription
10.0 years ago Julie Zhu ★ 4.3k
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4
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4.1k
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GRanges DitancetoNearest query
Transcription GenomicRanges Transcription GenomicRanges
updated 10.0 years ago by 13k • written 10.0 years ago by ▴ 150
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0
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701
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GOstats adding custom annotations
Transcription miRNA GO Transcription miRNA GO
10.1 years ago sudeep s ▴ 60
0
votes
2
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1.4k
views
goTools: Error in goidvect[test] : invalid subscript type \'list\'
Transcription Microarray Annotation GO goTools Transcription Microarray Annotation GO
updated 10.1 years ago by 60k • written 10.1 years ago by ★ 12k
0
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4
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1.1k
views
AffyID mapping question
Transcription mouse4302 Transcription mouse4302
updated 10.1 years ago by ★ 7.2k • written 10.1 years ago by ★ 12k
0
votes
11
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1.8k
views
"graphite" Biocarta 'native' graphs different from Biocarta web site?
Transcription Pathways Leukemia graphite Transcription Pathways Leukemia graphite
10.2 years ago Hamid Bolouri ▴ 90
0
votes
5
replies
1.0k
views
predicting transcription factors
Transcription Transcription
updated 10.2 years ago by ▴ 750 • written 10.2 years ago by ▴ 380
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0
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775
views
Biological Pathway Database
Transcription Pathways Category Transcription Pathways Category
10.3 years ago Gita Singh ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: IsoformSwitchAnalyzeR package on mouse data by bpshtiwan ▴ 10
Hello Ryan, Also, I am not able to find esemble file that has haplotype info in it. Kindly, have you solved the problem? Best
Comment: Design and contrast matrices for analyzing the effect of two factors of interest by Gordon Smyth 46k
I understand that your mock dataset has expression data for just one protein instead of 8000, but is the phenoData complete? Does your real…
Comment: error running UniProt.ws by James W. MacDonald 60k
Or maybe it is a quick fix! Nicely done Marcel!
Answer: Error with TCGA package - TCGAbiolinks by Tiago C. Silva ▴ 220
It is working with the github version. Could you update please? BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data") …
Comment: Error with TCGA package - TCGAbiolinks by Marcel Ramos 570
You can try the Genomic Data Commons Data Portal at [https://portal.gdc.cancer.gov/][1] or the `GenomicDataCommons` R/Bioconductor packag…
Votes
A: Importance of Order in Design Formula
remove microarray batch effects using Limma
On empirical Bayes of edgeR
Answer: CQN to DESeq2
Comment: package 'BiocInstaller' is not available (for R version 3.4.4)
Awards • All
Centurion to Marcel Ramos 570
Scholar to Gordon Smyth 46k
Popular Question to sunnykevin97 • 0
Popular Question to Alejandro Reyes ★ 1.8k
Popular Question to Leonardo Collado Torres ▴ 1000
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