Showing : transcription • reset
0
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12
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2.4k
views
more stupid *Ranges questions...
Transcription ChIPpeakAnno GenomicRanges Transcription ChIPpeakAnno GenomicRanges
updated 12.6 years ago by ★ 11k • written 12.6 years ago by ★ 4.2k
0
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11
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2.5k
views
"graphite" Biocarta 'native' graphs different from Biocarta web site?
Transcription Pathways Leukemia graphite Transcription Pathways Leukemia graphite
11.9 years ago Hamid Bolouri ▴ 90
0
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11
replies
2.2k
views
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
0
votes
7
replies
2.1k
views
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
0
votes
5
replies
1.5k
views
predicting transcription factors
Transcription Transcription
updated 11.9 years ago by ▴ 750 • written 11.9 years ago by ▴ 380
1
vote
5
replies
2.2k
views
paCalls oligo package
Transcription oligo Transcription oligo
updated 11.6 years ago by 65k • written 11.6 years ago by ▴ 190
0
votes
5
replies
2.2k
views
GO with R and Bioconductor
Transcription GO GOstats biomaRt topGO goseq Transcription GO GOstats biomaRt topGO
updated 13.2 years ago by 6.7k • written 13.2 years ago by ▴ 210
0
votes
5
replies
1.7k
views
Help with promoter analysis
Transcription convert biomaRt Transcription convert biomaRt
12.2 years ago Davy ▴ 20
0
votes
5
replies
1.4k
views
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
0
votes
5
replies
1.3k
views
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
1
vote
4
replies
1.5k
views
Is GO.db out of date?
Transcription GO Transcription GO
11.2 years ago • updated 11.1 years ago chawla ▴ 190
1
vote
4
replies
1.2k
views
DESeq2: Tests of log2 differences
deseq2 rna-seq transcription dgea
7.0 years ago • updated 6.9 years ago fabian ▴ 40
0
votes
4
replies
1.3k
views
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
0
votes
4
replies
4.8k
views
GRanges DitancetoNearest query
Transcription GenomicRanges Transcription GenomicRanges
updated 11.7 years ago by ★ 13k • written 11.7 years ago by ▴ 150
0
votes
4
replies
2.1k
views
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
0
votes
4
replies
1.5k
views
AffyID mapping question
Transcription mouse4302 Transcription mouse4302
updated 11.8 years ago by ★ 7.2k • written 11.9 years ago by ★ 13k
0
votes
4
replies
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
0
votes
4
replies
2.3k
views
PWMmatch: position weight matrix or position frequency matrix?
Transcription Transcription
updated 13.2 years ago by 16k • written 13.2 years ago by ▴ 10
0
votes
3
replies
2.3k
views
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
0
votes
3
replies
1.3k
views
retrieving genomic sequences with biomaRt
Transcription biomaRt Transcription biomaRt
updated 17.6 years ago by ▴ 580 • written 17.6 years ago by ★ 1.9k
0
votes
3
replies
1.1k
views
ChIPpeakAnno
Transcription ChIPpeakAnno Transcription ChIPpeakAnno
14.3 years ago • updated 14.2 years ago Julie Zhu ★ 4.3k
0
votes
3
replies
1.5k
views
matching transcription factor binding sites
Transcription Transcription
updated 16.1 years ago by 16k • written 16.1 years ago by ▴ 330
0
votes
3
replies
1.5k
views
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
0
votes
3
replies
1.5k
views
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
0
votes
3
replies
1.6k
views
limma: print-tip loess and empty spots
Transcription Normalization GUI limma Transcription Normalization GUI limma
updated 17.0 years ago by ▴ 50 • written 17.0 years ago by 50k
0
votes
2
replies
949
views
Transcription factor binding site information
Transcription Transcription
17.0 years ago Ольга Камнева ▴ 90
0
votes
2
replies
1.2k
views
clustering of genes
Transcription Clustering Cancer Transcription Clustering Cancer
updated 21.0 years ago by ★ 13k • written 21.0 years ago by 50k
0
votes
2
replies
4.7k
views
gplots Heatmap
SNP Transcription Sequencing RNASeq miRNA Microarray Annotation Normalization GO Cancer
updated 12.2 years ago by ★ 13k • written 12.2 years ago by ▴ 10
0
votes
2
replies
1.1k
views
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
votes
2
replies
2.1k
views
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
0
votes
2
replies
1.4k
views
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
votes
2
replies
2.7k
views
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
0
votes
2
replies
1.2k
views
How Does one subset a XStringView or PDict object?
Transcription BSgenome Biostrings BSgenome Transcription BSgenome Biostrings BSgenome
updated 13.3 years ago by 25k • written 13.3 years ago by ▴ 410
0
votes
2
replies
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
0
votes
2
replies
2.0k
views
Getting annotation into GOstat
Transcription Transcription
updated 6.2 years ago by • 0 • written 11.5 years ago by ★ 6.0k
0
votes
2
replies
3.8k
views
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
0
votes
2
replies
1.2k
views
matchPWM() questions
Transcription Transcription
updated 11.2 years ago by 16k • written 11.2 years ago by ▴ 340
0
votes
2
replies
2.2k
views
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
0
votes
2
replies
901
views
Querying/manipulating JASPAR data
Transcription Cancer Transcription Cancer
updated 13.9 years ago by ★ 1.7k • written 13.9 years ago by ★ 13k
0
votes
2
replies
1.0k
views
gDNA Cy3, cDNA Cy5
Transcription Biobase annotate Transcription Biobase annotate
updated 16.6 years ago by ★ 13k • written 16.6 years ago by ▴ 270
0
votes
2
replies
1.2k
views
how to use writeFASTA in modality "append"
Transcription miRNA Biostrings Transcription miRNA Biostrings
updated 14.8 years ago by 16k • written 14.8 years ago by ▴ 870
0
votes
2
replies
1.5k
views
exon and transcription start site locations
Transcription GO Transcription GO
updated 14.5 years ago by ▴ 620 • written 14.5 years ago by ▴ 180
0
votes
2
replies
841
views
normalization
Transcription Microarray Transcription Microarray
updated 20.0 years ago by ▴ 920 • written 20.0 years ago by ▴ 90
0
votes
2
replies
1.8k
views
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
0
votes
1
reply
980
views
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
0
votes
1
reply
838
views
about transcription factor binding site database
Transcription biomaRt Transcription biomaRt
updated 12.4 years ago by ★ 13k • written 12.4 years ago by ▴ 70
0
votes
1
reply
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
0
votes
1
reply
864
views
ChIPpeakAnno, makeVennDiagram
Transcription ChIPpeakAnno Transcription ChIPpeakAnno
12.5 years ago Julie Zhu ★ 4.3k
0
votes
1
reply
1.7k
views
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
0
votes
1
reply
1.5k
views
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
50 results • Page 1 of 1
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Answer: How to save the DEXSeq results by Michael Love 41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups by Robert Castelo ★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways" by James W. MacDonald 65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Answer: Trim/Filter out-of-bounds GRanges by Michael Love 41k
https://support.bioconductor.org/p/73432/#73448
Comment: Couldn't connect to server while using "pathways" by Michael Love 41k
You've put the tag "DESeq2" which results in an email to the maintainer, me, that I should respond to a post on the support site. Can you …
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
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