Showing : transcription • reset
0
votes
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
votes
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
votes
11
replies
2.1k
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
2.1k
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Is GO.db out of date?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
11.1 years ago chawla ▴ 190
1
vote
4
replies
1.2k
views
DESeq2: Tests of log2 differences
deseq2 rna-seq transcription dgea
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 15.5 years ago by 16k • written 15.5 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 11.8 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 7.5 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
14.2 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
1.4k
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 16.9 years ago by ▴ 50 • written 16.9 years ago by 50k
0
votes
2
replies
945
views
Transcription factor binding site information
Transcription Transcription
17.0 years ago Ольга Камнева ▴ 90
0
votes
2
replies
1.1k
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
1.1k
views
How Does one subset a XStringView or PDict object?
Transcription BSgenome Biostrings BSgenome Transcription BSgenome Biostrings BSgenome
updated 13.2 years ago by 25k • written 13.2 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
1.9k
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 11.1 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
899
views
Querying/manipulating JASPAR data
Transcription Cancer Transcription Cancer
updated 13.8 years ago by ★ 1.7k • written 13.8 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 14.4 years ago by ▴ 620 • written 14.4 years ago by ▴ 180
0
votes
2
replies
835
views
normalization
Transcription Microarray Transcription Microarray
updated 19.9 years ago by ▴ 920 • written 19.9 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
974
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
834
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
1000
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
861
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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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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