Showing : Transcription • reset
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Is there a Bioconductor package to calculate TFs regulatory networks?
TFs Transcription regulator
22 months ago OliverBoynton • 0
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1.9k
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Getting annotation into GOstat
Transcription Transcription
updated 6.2 years ago by • 0 • written 11.5 years ago by ★ 6.0k
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1.1k
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Reference annotation file contains only transcript and CDS information, how to analyze the different expression of genes?
transcription hisat2
6.4 years ago zoukai3412085 • 0
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Job: PhD computational position - Milan
epigenetics transcription computational biology Job
6.8 years ago mattia pelizzola ▴ 200
1
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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
6.9 years ago fabian ▴ 40
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917
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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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1
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1.3k
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TF ANALYSIS USING JASPAR
transcription jaspar
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 30
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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 7.5 years ago by • 0 • written 17.2 years ago by ▴ 580
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News: BioCAsia, 4th November 2016, Brisbane, Australia
conference transcription epigenomics visualization infrastructure News
7.8 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
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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
4
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0
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1.5k
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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
0
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1
reply
2.5k
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Interspecies differential expression of orthologs with Edger
Transcription edgeR Transcription edgeR
9.7 years ago Tim Triche ★ 4.2k
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11
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2.1k
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Interspecies differential expression of orthologs with Edger
Transcription edgeR Transcription edgeR
updated 9.7 years ago by 50k • written 9.7 years ago by ▴ 140
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rsqlite for windows from fhcrc
Transcription BiocInstaller Transcription BiocInstaller
updated 9.7 years ago by 25k • written 9.7 years ago by ★ 6.5k
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1.3k
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Useful information about Ensembl release 76 mart databases
Transcription zebrafish Transcription zebrafish
9.7 years ago Thomas Maurel ▴ 800
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1
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1.7k
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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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1.2k
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An. Gambie RNA-Seq differential expression using gage and pathview
Transcription Normalization gage Transcription Normalization gage
9.8 years ago Saul Lozano ▴ 20
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4
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1.3k
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Limma package and minimal number of genes
Transcription limma Transcription limma
updated 9.9 years ago by ★ 1.3k • written 9.9 years ago by ▴ 10
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1.2k
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total count filter cutoff
Transcription Transcription
updated 10.0 years ago by ▴ 20 • written 10.0 years ago by ★ 13k
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1
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2.2k
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Deseq2-help
Transcription DESeq DESeq2 Transcription DESeq DESeq2
updated 10.1 years ago by ▴ 30 • written 10.1 years ago by 41k
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question on MotifDb package
Transcription MotifDb Transcription MotifDb
10.1 years ago Paul Shannon ▴ 470
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7
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2.1k
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Low number of replicates DESeq
Transcription GO DESeq2 Transcription GO DESeq2
updated 10.2 years ago by 41k • written 10.1 years ago by ▴ 130
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0
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1.4k
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questions related to DiffBind package
Transcription Normalization DiffBind Transcription Normalization DiffBind
10.2 years ago Rory Stark ★ 5.1k
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1
reply
1.6k
views
DiffBind loading Problem
Transcription ChIPSeq chipseq DiffBind Transcription ChIPSeq chipseq DiffBind
10.2 years ago Rory Stark ★ 5.1k
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4
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1.5k
views
Rcade analysis without ChIP-seq replicates
Transcription Rcade Transcription Rcade
updated 10.2 years ago by ▴ 60 • written 10.2 years ago by ▴ 30
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2
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2.2k
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ensemblVEP, variant_effect_predictor versions and release schedule
Transcription HapMap PolyPhen SIFT convert genomes ensemblVEP Transcription HapMap SIFT
updated 10.3 years ago by ★ 6.8k • written 10.3 years ago by ▴ 30
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1
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1.9k
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Analysis of Affymetrix Human Gene 2.0 ST arrays
Transcription Annotation Normalization GO hgu133plus2 affy PROcess Category Transcription
updated 10.4 years ago by ▴ 80 • written 10.4 years ago by ▴ 20
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Bioconductor 2.13 is released
BiocViews aCGH SNP Transcription Sequencing miRNA Microarray Genetics Proteomics Coverage
10.5 years ago Dan Tenenbaum ★ 8.2k
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DNaseR - a new Bioconductor package for DNase-seq digital genomic footprinting
Transcription DNaseR Transcription DNaseR
10.5 years ago Pedro Madrigal ▴ 20
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DiffBind questions
Transcription Cancer DiffBind MMDiff Transcription Cancer DiffBind MMDiff
10.7 years ago Rory Stark ★ 5.1k
0
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2
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3.7k
views
TranscriptDb of GENCODE Genes
Transcription Annotation Transcription Annotation
updated 10.7 years ago by ★ 7.2k • written 10.7 years ago by ★ 1.5k
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
11.1 years ago chawla ▴ 190
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2
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1.2k
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matchPWM() questions
Transcription Transcription
updated 11.1 years ago by 16k • written 11.1 years ago by ▴ 340
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1.1k
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BitSeq: Required input for 3' bias correction on transcripts.
Transcription RNASeq safe BitSeq Transcription RNASeq safe BitSeq
11.2 years ago Peter Glaus ▴ 70
0
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1
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1.7k
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promoter prediction
Transcription MotIV MotifDb Transcription MotIV MotifDb
updated 11.4 years ago by ▴ 380 • written 11.4 years ago by ▴ 750
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ComBat
Transcription Genetics Pathways Network Survival Cancer Breast Colon Kidney Leukemia HIV
11.5 years ago SSc Array Core ▴ 10
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3.1k
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Bioconductor 2.11 is released
BiocViews SNP Transcription Sequencing miRNA Microbiome Microarray qPCR Genetics Coverage
11.6 years ago Dan Tenenbaum ★ 8.2k
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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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1
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1.8k
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Bioconductor Digest, Vol 115, Issue 22
Transcription Sequencing miRNA SmallRNA Annotation Normalization GO Cancer Organism edgeR
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ▴ 10
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1.3k
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NGS public data analysis
Transcription DEGseq Transcription DEGseq
11.6 years ago Jill Pleasance ▴ 10
0
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1
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1.5k
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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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923
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ChIPpeakAnno - c elegans annotation feature type: translation start site
Transcription Transcription
11.7 years ago Julie Zhu ★ 4.3k
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4
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4.8k
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GRanges DitancetoNearest query
Transcription GenomicRanges Transcription GenomicRanges
updated 11.7 years ago by ★ 13k • written 11.7 years ago by ▴ 150
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0
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937
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GOstats adding custom annotations
Transcription miRNA GO Transcription miRNA GO
11.8 years ago sudeep s ▴ 60
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2
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1.8k
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goTools: Error in goidvect[test] : invalid subscript type \'list\'
Transcription Microarray Annotation GO goTools Transcription Microarray Annotation GO
updated 11.8 years ago by 65k • written 11.8 years ago by ★ 13k
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4
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1.5k
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AffyID mapping question
Transcription mouse4302 Transcription mouse4302
updated 11.8 years ago by ★ 7.2k • written 11.8 years ago by ★ 13k
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11
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2.5k
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"graphite" Biocarta 'native' graphs different from Biocarta web site?
Transcription Pathways Leukemia graphite Transcription Pathways Leukemia graphite
11.9 years ago Hamid Bolouri ▴ 90
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5
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1.5k
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predicting transcription factors
Transcription Transcription
updated 11.9 years ago by ▴ 750 • written 11.9 years ago by ▴ 380
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1.1k
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Biological Pathway Database
Transcription Pathways Category Transcription Pathways Category
12.0 years ago Gita Singh ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k
an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.
Comment: Trying to use enrichGO by Guido Hooiveld ★ 3.9k
Nothing would prevent you from using the `enrichGO` function (or any other function for over-representation analysis [ORA]) with only 14 ge…
Comment: Different Shrunk Log2FC according with reference by andrebolerbarros ▴ 20
Thanks @atpoint for your answer! The issue with that is then it severely hinders the possiblity of using `apeglm` shrinking approach, sinc…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by ATpoint ★ 4.0k
The error that is relevant is `Aborted (core dumped)`. This line 2890 refers to the C source code that throws the error, it is not relevant…
Answer: Different Shrunk Log2FC according with reference by ATpoint ★ 4.0k
Please see: https://support.bioconductor.org/p/p134551/ I asked basically the same before. In short, reference level might have an influ…
Votes
DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds
Subset DEXSeqDataSet In DEXSeq
How to get all possible comparisons in DiffBind
Comment: get BM error
Answer: Citation for edgeR user guide
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