Showing : Sequencing • reset
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News: Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing Sequencing SequencingData
6 days ago communication • 0
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is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
6 months ago Sara • 0
2
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5
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1.4k
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Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
19 months ago Marcus • 0
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1
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1.3k
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dispersion in edgeR
Sequencing edgeR Sequencing edgeR
updated 22 months ago by 50k • written 13.8 years ago by ★ 6.0k
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Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
2.2 years ago Robert Castelo ★ 3.2k
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1.4k
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Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
2.5 years ago ary.lech ▴ 10
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995
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Job: Bioinformatician position at University of Texas Southwestern Medical Center
Sequencing bioinformatics
2.5 years ago chao.xing • 0
1
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3
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868
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Preferential sequencing of longer Genes in Illumina?
DESeq2 sequencing
updated 3.1 years ago by • 0 • written 3.1 years ago by • 0
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816
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is the P value reliable if the counts are Low across the sample ?
DESeq2 sequencing
3.1 years ago simplyphage • 0
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941
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Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
3.2 years ago Robert Castelo ★ 3.2k
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1.1k
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Job: Post-doc position in multi-omics of Alzheimer's disease at Columbia University in New York City
JobPosting postdoc sequencing multiomics
3.2 years ago • updated 3.1 years ago lhd • 0
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873
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Job: Scientist/Senior Scientist, Statistical Geneticist
Sequencing Genetics GeneticsPed statistics
3.3 years ago António Miguel de Jesus Domingues ▴ 490
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888
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Job: Postdoc: BIOINFORMATICS FOR FUNCTIONAL GENOMICS AND POPULATION GENETICS OF CANCER
GWAS lung cancer functional genomics eQTL sequencing Job
4.0 years ago jiyeon.choi2 • 0
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901
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Job: Post-doc fellow - Aparicio Lab
single cell bioinformatics genome sequencing Job
4.6 years ago jmaanaki • 0
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2
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1.3k
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DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
4.8 years ago zhigang.li • 0
2
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3
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1.4k
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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
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1
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812
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Annotating protein sequences
Protein iranges sequencing
5.1 years ago ieuangw • 0
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2.6k
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Job: Postdoc in Population Genomics - UC Davis
bioinformatics evolution sequencing genome analysis genomics Job
5.5 years ago hschmidt • 0
0
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0
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977
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Job: Research Associate- Production Bioinformatics - Atlantic Cancer Research Institute - Moncton -New Brunwsiwck - Canada
cancer bioinformatics bioinformatician job sequencing Job
5.7 years ago gabriel.wajnberg • 0
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10
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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
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1.1k
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Job: Post-doc in Prostate Cancer Research (Statistics / Computational Biology) at University of St Andrews (+PhD position also available)
cancer sequencing rnaseq methylation smallrna Job
5.8 years ago Andy Lynch ▴ 120
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821
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Number of reads needed for Guide-Seq
sequencing
6.0 years ago Jacques-P.Tremblay • 0
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1
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2.7k
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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
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906
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Sequence composition effect
sequencing rnaseq_analysis
6.2 years ago alemutak • 0
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1
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1.8k
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write ab1 files
sangerseqr sequencing abi
6.6 years ago tmolosh • 0
2
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11
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1.9k
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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
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1.7k
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Job: Postdoc / Computational Biologist for circulating tumor DNA/RNA profiling at Memorial Sloan Kettering Cancer Center MSKCC, New York
cancer sequencing genetics genomes diagnostic Job
7.6 years ago dtlabmskcc • 0
3
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8
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4.4k
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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
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2.2k
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Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 7.6 years ago by • 0 • written 14.0 years ago by ★ 1.6k
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2
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3.5k
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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
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4
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1.5k
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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
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4
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2.8k
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DNAString: Standard checksum function?
Biostrings FASTA sequencing
8.1 years ago Henrik Bengtsson ★ 2.4k
2
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4
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1.4k
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Complex ANOVA analysis in EdgeR
edger anova sequencing
updated 8.2 years ago by ★ 28k • written 8.2 years ago by • 0
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5
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2.2k
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getting sample size for RNAseq experiment
rnaseqpower sspa sample size sequencing complex-design
updated 8.2 years ago by ▴ 20 • written 8.2 years ago by • 0
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4
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1.6k
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IONiseR readFast5Summary Error
R sequencing preprocessing bioconductor
updated 8.3 years ago by ★ 6.5k • written 8.4 years ago by • 0
1
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1.7k
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Job: Post-doc Position in Epigenetic Bioinformatics
cancer sequencing epigenetics computational biology bioinformatics Job
8.4 years ago Yassen Assenov ▴ 10
1
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1
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2.4k
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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
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2.1k
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DNAcopy: Using log-ratios and B-allele frequencies
sequencing snp
updated 8.6 years ago by ▴ 20 • written 8.6 years ago by • 0
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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
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2.2k
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Perplexing results with Limma with RNA-seq data
sequencing microarray
updated 8.7 years ago by ★ 13k • written 8.7 years ago by ▴ 420
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1.7k
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News: BioCAsia, 8 Sept 2015, Tokyo
sequencing transcription epigenomics visualization infrastructure News
8.8 years ago • updated 8.7 years ago Matthew Ritchie ▴ 1000
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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
3
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1
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2.3k
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Adjusting for gender using limma
limma microarray sequencing
updated 8.7 years ago by 65k • written 8.7 years ago by ▴ 420
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1
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1.5k
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Getting data on the out-of-frame transcripts
annotate sequencing genomicfeatures
updated 8.7 years ago by 16k • written 8.7 years ago by • 0
3
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4
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3.4k
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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
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2
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3.8k
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Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 8.8 years ago by • 0 • written 11.0 years ago by ★ 8.2k
4
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2
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2.2k
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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
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3
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1.7k
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SVA batch effects for different technologies
normalization deseq2 sequencing sva
8.8 years ago marcin.bazyliszek • 0
4
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1.5k
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News: Hands-on Bioconductor course, 7 Sept 2015, Tokyo
sequencing transcription variantfiltering annotation News
8.8 years ago Matthew Ritchie ▴ 1000
2
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4
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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
50 results • Page 1 of 1
Recent ...
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it always helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR? Are you starting with…
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 doctor know about Alzheimer and they don't expect significan…
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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