Showing : Sequencing • reset
8
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2
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3.5k
views
Appropriate ways to filter counts data for voom/limma
limma edger sequencing
updated 7.7 years ago by 50k • written 7.7 years ago by ▴ 10
6
votes
6
replies
1.4k
views
Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
2.5 years ago ary.lech ▴ 10
6
votes
1
reply
3.0k
views
[ReportingTools] HTMLReport of DESeq2 results using Ensembl Gene Ids
Sequencing Annotation convert biomaRt ReportingTools DESeq2 Sequencing Annotation convert
updated 9.3 years ago by ▴ 370 • written 10.4 years ago by ▴ 160
6
votes
4
replies
1.5k
views
How to normalize chemical genomics barcode sequencing data
limma normalization sequencing edger
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 20
5
votes
2
replies
3.1k
views
Gviz - show plus and minus strand from a bam
Sequencing Coverage Gviz Sequencing Coverage Gviz
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by ▴ 490
4
votes
2
replies
2.2k
views
Detect global differences in miRNA expression between tumor and normal using spike-ins
edger limma mirna sequencing
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 40
4
votes
0
replies
1.5k
views
News: Hands-on Bioconductor course, 7 Sept 2015, Tokyo
sequencing transcription variantfiltering annotation News
8.8 years ago Matthew Ritchie ▴ 1000
3
votes
0
replies
1.7k
views
News: BioCAsia, 8 Sept 2015, Tokyo
sequencing transcription epigenomics visualization infrastructure News
8.8 years ago • updated 8.7 years ago Matthew Ritchie ▴ 1000
3
votes
3
replies
2.9k
views
Clarrification of ReadDNAStringSet
sequencing
9.2 years ago khouloud.madbouh • 0
3
votes
4
replies
3.4k
views
Variance filtering prior to RNA-seq differential expression
sequencing deseq limma
updated 8.8 years ago by 50k • written 8.8 years ago by ▴ 420
3
votes
8
replies
4.4k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing DESeq Sequencing DESeq
updated 7.6 years ago by • 0 • written 10.3 years ago by ★ 13k
3
votes
1
reply
2.3k
views
Adjusting for gender using limma
limma microarray sequencing
updated 8.7 years ago by 65k • written 8.7 years ago by ▴ 420
2
votes
3
replies
1.4k
views
Boxplot function not showing all reads length on x-axis
boxplot reads fastq sequencing rsubread
updated 4.9 years ago by ★ 3.6k • written 4.9 years ago by ▴ 60
2
votes
5
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1.4k
views
Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
19 months ago Marcus • 0
2
votes
4
replies
1.4k
views
Complex ANOVA analysis in EdgeR
edger anova sequencing
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
2
votes
11
replies
1.9k
views
DESeq2 polysome profiling analysis with 2 interaction terms
deseq2 sequencing polysome profiling
updated 6.9 years ago by 41k • written 6.9 years ago by ▴ 10
2
votes
4
replies
6.8k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing Alignment DESeq DESeq2 Sequencing Alignment DESeq DESeq2
updated 8.9 years ago by • 0 • written 9.9 years ago by ★ 13k
2
votes
0
replies
2.2k
views
Job: Job Opening: Computational Biologist @ Genentech Bioinformatics
Job Sequencing Genetics Cancer
updated 9.6 years ago by ★ 8.2k • written 9.6 years ago by ★ 11k
2
votes
2
replies
816
views
is the P value reliable if the counts are Low across the sample ?
DESeq2 sequencing
3.1 years ago simplyphage • 0
2
votes
5
replies
1.5k
views
DEXSeq update results change
Sequencing DESeq DEXSeq Sequencing DESeq DEXSeq
9.7 years ago António Miguel de Jesus Domingues ▴ 490
2
votes
3
replies
1.7k
views
SVA batch effects for different technologies
normalization deseq2 sequencing sva
8.8 years ago marcin.bazyliszek • 0
1
vote
2
replies
1.3k
views
Can I use rtracklayer to get the sequence surrounding a set of variants?
rtracklayer sequencing reference genome
8.6 years ago Stephanie M. Gogarten ▴ 870
1
vote
3
replies
868
views
Preferential sequencing of longer Genes in Illumina?
DESeq2 sequencing
updated 3.1 years ago by • 0 • written 3.1 years ago by • 0
1
vote
0
replies
2.4k
views
dispersion in edgeR
Sequencing edgeR
13.8 years ago • updated 22 months ago Gordon Smyth 50k
1
vote
1
reply
2.7k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R sequencing alignment rsamtools mapping
updated 6.0 years ago by 65k • written 6.0 years ago by ▴ 10
1
vote
0
replies
1.7k
views
Job: Post-doc Position in Epigenetic Bioinformatics
cancer sequencing epigenetics computational biology bioinformatics Job
8.4 years ago Yassen Assenov ▴ 10
1
vote
10
replies
2.1k
views
Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
deseq2 sequencing ribosome profiling riboseq multiple factor design
updated 5.7 years ago by 41k • written 5.7 years ago by ▴ 10
1
vote
1
reply
2.2k
views
Perplexing results with Limma with RNA-seq data
sequencing microarray
updated 8.7 years ago by ★ 13k • written 8.7 years ago by ▴ 420
1
vote
2
replies
2.1k
views
DNAcopy: Using log-ratios and B-allele frequencies
sequencing snp
updated 8.6 years ago by ▴ 20 • written 8.6 years ago by • 0
1
vote
1
reply
2.4k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing biostrings shortread
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 10
1
vote
0
replies
1.3k
views
Genome editing analysis with Illumina sequencing
indel sequencing alignment
9.0 years ago Merienne Nicolas ▴ 120
1
vote
2
replies
3.0k
views
Interaction categorical/continuous variable DESeq2
Sequencing DESeq2
updated 9.6 years ago by ★ 13k • written 9.6 years ago by ▴ 80
1
vote
0
replies
1.4k
views
Job: PI position at EMBL-EBI (Cambridge UK)
Job Sequencing
9.6 years ago Wolfgang Huber ★ 13k
1
vote
2
replies
2.1k
views
DESeqs two-factor two-level, interaction is interested
Sequencing GO phyloseq DESeq2 Sequencing GO phyloseq DESeq2
updated 9.8 years ago by 41k • written 9.8 years ago by ▴ 60
1
vote
2
replies
1.2k
views
Please help: SNP Frequency Analysis Package in Bioconductor
Sequencing Sequencing
updated 12.1 years ago by 6.7k • written 12.1 years ago by ▴ 200
1
vote
1
reply
1.2k
views
Rsubread for paired end SOLID sequencing
Sequencing Alignment convert Rsubread Sequencing Alignment convert Rsubread
updated 10.6 years ago by ★ 3.6k • written 10.6 years ago by ▴ 50
0
votes
0
replies
1.8k
views
Differential gene expression: EdgeR / DESeq and identifying noise/outliers
Sequencing edgeR DESeq Sequencing edgeR DESeq
11.8 years ago Gordon Smyth 50k
0
votes
1
reply
631
views
R package to estimate aggregation of NGS reads
Sequencing Sequencing
updated 15.6 years ago by 25k • written 15.6 years ago by ▴ 340
0
votes
2
replies
1.6k
views
preparing sequencing data for use with anota
Sequencing Normalization PROcess anota Sequencing Normalization PROcess anota
updated 8.7 years ago by • 0 • written 10.1 years ago by ★ 13k
0
votes
1
reply
638
views
Bioconductor and sequencing
Sequencing Cancer Sequencing Cancer
updated 15.6 years ago by ▴ 150 • written 15.6 years ago by ★ 5.5k
0
votes
0
replies
1.1k
views
Postdoctoral position available at Stellenbosch University
Sequencing Genetics Pharmacogenomics Sequencing Genetics Pharmacogenomics
12.0 years ago Warnich, Louise <lw@sun.ac.za> ▴ 10
0
votes
3
replies
1.9k
views
Diffbind: Binding Affinity Heatmap
Sequencing GO Clustering GLAD edgeR DESeq DiffBind Sequencing GO Clustering GLAD edgeR
10.7 years ago Rory Stark ★ 5.1k
0
votes
0
replies
958
views
New Bioconductor package: rtracklayer
Sequencing Annotation CGH GenomeGraphs rtracklayer Sequencing Annotation CGH GenomeGraphs
16.0 years ago Michael Lawrence ▴ 620
0
votes
0
replies
1.3k
views
Two Computational Biology / Bioinformatics Positions, University of Cambridge, UK
Sequencing Sequencing
16.0 years ago Krys Kelly ▴ 270
0
votes
0
replies
729
views
Chip-seq pipeline and cloud ami questions
Sequencing Microarray edgeR Sequencing Microarray edgeR
10.9 years ago Christopher Howerton ▴ 40
0
votes
0
replies
1.5k
views
JOB: Cancer Research UK - Cambridge Research Institute Bioinformatics Core
Sequencing Microarray Cancer Sequencing Microarray Cancer
14.8 years ago Mark Dunning ★ 1.1k
0
votes
0
replies
1.1k
views
Postdoctoral Research @ Cold Spring Harbor Laboratory
Sequencing Genetics Cancer Sequencing Genetics Cancer
16.1 years ago Matthew Vaughn ▴ 30
0
votes
0
replies
1.7k
views
Post-doc position in Paris
Sequencing Epigenetics Cancer Breast DECIPHER Sequencing Epigenetics Cancer Breast
14.8 years ago Joern Toedling ▴ 450
0
votes
0
replies
893
views
Call for participants of CAMDA2009
Sequencing Sequencing
14.9 years ago Pan Du ★ 1.2k
0
votes
0
replies
809
views
bioc-sig-sequencing: new list for Bioconductor high-throughput sequencing analysis
Sequencing Sequencing
16.1 years ago Martin Morgan 25k
50 results • Page 1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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