Showing : transcription • reset
0
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4
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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
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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
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
1
vote
4
replies
1.5k
views
Is GO.db out of date?
Transcription GO Transcription GO
11.1 years ago chawla ▴ 190
0
votes
2
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2.1k
views
PWM matching using matchPWM in Biostrings
Transcription BSgenome Biostrings BSgenome Transcription BSgenome Biostrings BSgenome
updated 14.9 years ago by ★ 1.6k • written 14.9 years ago by ▴ 10
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
0
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2
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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
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1.4k
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chip-seq data analysis
Transcription ChIPSeq Alignment chipseq Transcription ChIPSeq Alignment chipseq
updated 14.1 years ago by 21k • written 14.1 years ago by ▴ 60
0
votes
3
replies
1.4k
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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
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3
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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
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
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
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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
5
replies
1.7k
views
Help with promoter analysis
Transcription convert biomaRt Transcription convert biomaRt
12.2 years ago Davy ▴ 20
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
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
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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
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
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
3
replies
1.1k
views
ChIPpeakAnno
Transcription ChIPpeakAnno Transcription ChIPpeakAnno
14.2 years ago Julie Zhu ★ 4.3k
0
votes
2
replies
943
views
Transcription factor binding site information
Transcription Transcription
17.0 years ago Ольга Камнева ▴ 90
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
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
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
1
reply
998
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
1.5k
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
0
votes
1
reply
849
views
annotation - 1 probe with 2 UG ??
Transcription Annotation GO hgu133a probe Transcription Annotation GO hgu133a probe
updated 19.7 years ago by ★ 2.9k • written 19.7 years ago by ▴ 300
0
votes
1
reply
971
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
12
replies
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
1
reply
1.7k
views
PhD position available in Innsbruck, Austria
Transcription Microarray Cancer Leukemia Transcription Microarray Cancer Leukemia
12.4 years ago Johannes Rainer ▴ 80
0
votes
1
reply
967
views
concurrent R-release & R-devel versions -- bioc also? [was Re: from TF DNA binding motif to downstream genes?]
Transcription GO celegans BSgenome Biostrings BSgenome IRanges Transcription GO celegans
updated 14.2 years ago by 21k • written 14.2 years ago by ★ 1.1k
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
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
1
reply
977
views
TSS Regions
Transcription IRanges Transcription IRanges
updated 14.4 years ago by ★ 4.3k • written 14.4 years ago by ▴ 130
0
votes
1
reply
1.2k
views
Help with Oligo Package: Extracting and Graphing
Transcription Normalization Yeast probe affy graph tilingArray oligo pdInfoBuilder Starr
updated 14.5 years ago by ▴ 430 • written 14.5 years ago by ▴ 410
0
votes
1
reply
1.0k
views
question about ontoCompare() performance change
Transcription GO hgu133a goTools Transcription GO hgu133a goTools
updated 14.5 years ago by ★ 7.4k • written 14.5 years ago by ▴ 50
0
votes
2
replies
833
views
normalization
Transcription Microarray Transcription Microarray
updated 19.9 years ago by ▴ 920 • written 19.9 years ago by ▴ 90
0
votes
3
replies
1.5k
views
matching transcription factor binding sites
Transcription Transcription
updated 16.0 years ago by 16k • written 16.0 years ago by ▴ 330
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
1
reply
597
views
How can I trace back transcription target genes from the miRNAs file downloadable from miRbase ?
Transcription miRNA Transcription miRNA
updated 14.6 years ago by 21k • written 14.6 years ago by ▴ 870
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
1
reply
894
views
TilingArray Normalization
Transcription Normalization probe tilingArray Transcription Normalization probe tilingArray
updated 15.4 years ago by ★ 13k • written 15.4 years ago by ▴ 90
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
1
reply
738
views
over-representation of specific transcription factors in gene lists
Transcription Annotation GO Transcription Annotation GO
updated 16.7 years ago by ★ 7.4k • written 16.7 years ago by ▴ 830
0
votes
1
reply
1.2k
views
R: how to use writeFASTA in modality "append"
Transcription miRNA Biostrings Transcription miRNA Biostrings
updated 14.8 years ago by ★ 13k • written 14.8 years ago by ▴ 870
0
votes
1
reply
1.2k
views
R: Degradation plots - Affy package
Transcription qPCR Genetics probe affy Transcription qPCR Genetics probe affy
updated 17.6 years ago by ▴ 360 • written 17.6 years ago by ▴ 10
0
votes
1
reply
1.1k
views
question about ontoCompare() performance change
Transcription GO hgu133a goTools Transcription GO hgu133a goTools
updated 14.9 years ago by ▴ 60 • written 14.9 years ago by ▴ 50
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
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
50 results • Page 1 of 1
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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