Showing : Sequencing • reset
8
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2
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3.6k
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
3.1k
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 7.9 years ago by ★ 28k • written 7.9 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 10.5 years ago by ★ 1.6k • written 10.5 years ago by ▴ 510
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
8.9 years ago Matthew Ritchie ▴ 1000
3
votes
0
replies
1.7k
views
News: BioCAsia, 8 Sept 2015, Tokyo
sequencing transcription epigenomics visualization infrastructure News
8.9 years ago • updated 8.8 years ago Matthew Ritchie ▴ 1000
3
votes
3
replies
2.9k
views
Clarrification of ReadDNAStringSet
sequencing
9.3 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
4.5k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing DESeq Sequencing DESeq
updated 7.7 years ago by • 0 • written 10.4 years ago by ★ 13k
3
votes
1
reply
2.3k
views
Adjusting for gender using limma
limma microarray sequencing
updated 8.8 years ago by 65k • written 8.8 years ago by ▴ 420
2
votes
3
replies
1.5k
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
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5
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1.5k
views
Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
20 months ago Marcus • 0
2
votes
4
replies
1.5k
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 42k • written 6.9 years ago by ▴ 10
2
votes
4
replies
6.9k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing Alignment DESeq DESeq2 Sequencing Alignment DESeq DESeq2
updated 8.9 years ago by • 0 • written 10.0 years ago by ★ 13k
2
votes
0
replies
2.2k
views
Job: Job Opening: Computational Biologist @ Genentech Bioinformatics
Job Sequencing Genetics Cancer
updated 9.7 years ago by ★ 8.2k • written 9.7 years ago by ★ 11k
2
votes
2
replies
835
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
1.6k
views
DEXSeq update results change
Sequencing DESeq DEXSeq Sequencing DESeq DEXSeq
9.7 years ago António Miguel de Jesus Domingues ▴ 510
2
votes
3
replies
1.7k
views
SVA batch effects for different technologies
normalization deseq2 sequencing sva
8.9 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
8.7 years ago Stephanie M. Gogarten ▴ 870
1
vote
3
replies
886
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
13.9 years ago • updated 23 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
8.5 years ago Yassen Assenov ▴ 10
1
vote
10
replies
2.2k
views
Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
deseq2 sequencing ribosome profiling riboseq multiple factor design
updated 5.8 years ago by 42k • written 5.8 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
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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 8.5 years ago by 25k • written 8.5 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
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3.0k
views
Interaction categorical/continuous variable DESeq2
Sequencing DESeq2
updated 9.7 years ago by ★ 13k • written 9.7 years ago by ▴ 80
1
vote
0
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1.4k
views
Job: PI position at EMBL-EBI (Cambridge UK)
Job Sequencing
9.7 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 9.9 years ago by 42k • written 9.9 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 10.7 years ago by ★ 3.6k • written 10.7 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
11.9 years ago Gordon Smyth 50k
0
votes
1
reply
635
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
1.7k
views
preparing sequencing data for use with anota
Sequencing Normalization PROcess anota Sequencing Normalization PROcess anota
updated 8.8 years ago by • 0 • written 10.1 years ago by ★ 13k
0
votes
1
reply
651
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
12.1 years ago Warnich, Louise <lw@sun.ac.za> ▴ 10
0
votes
3
replies
2.0k
views
Diffbind: Binding Affinity Heatmap
Sequencing GO Clustering GLAD edgeR DESeq DiffBind Sequencing GO Clustering GLAD edgeR
10.7 years ago Rory Stark ★ 5.2k
0
votes
0
replies
972
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
16.1 years ago Krys Kelly ▴ 270
0
votes
0
replies
733
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Chip-seq pipeline and cloud ami questions
Sequencing Microarray edgeR Sequencing Microarray edgeR
11.0 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
14.9 years ago Joern Toedling ▴ 450
0
votes
0
replies
901
views
Call for participants of CAMDA2009
Sequencing Sequencing
15.0 years ago Pan Du ★ 1.2k
0
votes
0
replies
821
views
bioc-sig-sequencing: new list for Bioconductor high-throughput sequencing analysis
Sequencing Sequencing
16.2 years ago Martin Morgan 25k
50 results • Page 1 of 1
Recent ...
Replies
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix with the W covariates, to compute precision weights but not to adjust the log-cp…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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