Showing : sequencing • reset
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News: Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing Sequencing SequencingData
7 months ago communication • 0
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518
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is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
13 months ago Sara • 0
2
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5
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1.9k
views
Merge GRanges, ignore strand
Sequencing SummarizedExperiment GRanges
2.2 years ago Marcus • 0
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1
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1.5k
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dispersion in edgeR
Sequencing edgeR Sequencing edgeR
updated 2.5 years ago by 51k • written 14.4 years ago by ★ 6.0k
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929
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Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
2.8 years ago Robert Castelo ★ 3.4k
6
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6
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1.9k
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Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
3.1 years ago ary.lech ▴ 10
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0
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1.2k
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Job: Bioinformatician position at University of Texas Southwestern Medical Center
Sequencing bioinformatics
3.1 years ago chao.xing • 0
1
vote
3
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1.0k
views
Preferential sequencing of longer Genes in Illumina?
DESeq2 sequencing
updated 3.7 years ago by • 0 • written 3.7 years ago by • 0
2
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2
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993
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is the P value reliable if the counts are Low across the sample ?
DESeq2 sequencing
3.7 years ago simplyphage • 0
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1.1k
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Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
3.8 years ago Robert Castelo ★ 3.4k
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0
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1.4k
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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
3.8 years ago • updated 3.7 years ago lhd • 0
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1.1k
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Job: Scientist/Senior Scientist, Statistical Geneticist
Sequencing Genetics GeneticsPed statistics
3.9 years ago António Miguel de Jesus Domingues ▴ 510
0
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0
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1.1k
views
Job: Postdoc: BIOINFORMATICS FOR FUNCTIONAL GENOMICS AND POPULATION GENETICS OF CANCER
GWAS lung cancer functional genomics eQTL sequencing Job
4.6 years ago jiyeon.choi2 • 0
0
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0
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1.1k
views
Job: Post-doc fellow - Aparicio Lab
single cell bioinformatics genome sequencing Job
5.2 years ago jmaanaki • 0
0
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2
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1.5k
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DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
5.4 years ago zhigang.li • 0
2
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3
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1.7k
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Boxplot function not showing all reads length on x-axis
boxplot reads fastq sequencing rsubread
updated 5.5 years ago by ★ 3.6k • written 5.5 years ago by ▴ 60
0
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1
reply
971
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Annotating protein sequences
Protein iranges sequencing
5.7 years ago ieuangw • 0
0
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0
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3.0k
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Job: Postdoc in Population Genomics - UC Davis
bioinformatics evolution sequencing genome analysis genomics Job
6.1 years ago hschmidt • 0
0
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0
replies
1.2k
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Job: Research Associate- Production Bioinformatics - Atlantic Cancer Research Institute - Moncton -New Brunwsiwck - Canada
cancer bioinformatics bioinformatician job sequencing Job
6.3 years ago gabriel.wajnberg • 0
1
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10
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2.4k
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Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
deseq2 sequencing ribosome profiling riboseq multiple factor design
updated 6.3 years ago by 42k • written 6.3 years ago by ▴ 10
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0
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1.3k
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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
6.4 years ago Andy Lynch ▴ 120
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0
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961
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Number of reads needed for Guide-Seq
sequencing
6.6 years ago Jacques-P.Tremblay • 0
1
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1
reply
3.4k
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Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R sequencing alignment rsamtools mapping
updated 6.6 years ago by 67k • written 6.6 years ago by ▴ 10
0
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0
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1.0k
views
Sequence composition effect
sequencing rnaseq_analysis
6.8 years ago alemutak • 0
0
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1
reply
2.2k
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write ab1 files
sangerseqr sequencing abi
7.2 years ago tmolosh • 0
2
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11
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2.2k
views
DESeq2 polysome profiling analysis with 2 interaction terms
deseq2 sequencing polysome profiling
updated 7.5 years ago by 42k • written 7.5 years ago by ▴ 10
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0
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1.9k
views
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
8.2 years ago dtlabmskcc • 0
3
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8
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4.8k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing DESeq Sequencing DESeq
updated 8.2 years ago by • 0 • written 10.9 years ago by ★ 13k
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7
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2.5k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 8.2 years ago by • 0 • written 14.6 years ago by ★ 1.6k
8
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3
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4.1k
views
Appropriate ways to filter counts data for voom/limma
limma edger sequencing
written 8.3 years ago by ▴ 10
6
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4
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1.7k
views
How to normalize chemical genomics barcode sequencing data
limma normalization sequencing edger
updated 8.4 years ago by ★ 28k • written 8.4 years ago by ▴ 20
0
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5
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3.2k
views
DNAString: Standard checksum function?
Biostrings FASTA sequencing
8.7 years ago • updated 6 months ago Henrik Bengtsson ★ 2.4k
2
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4
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1.6k
views
Complex ANOVA analysis in EdgeR
edger anova sequencing
updated 8.7 years ago by ★ 28k • written 8.7 years ago by • 0
0
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5
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2.5k
views
getting sample size for RNAseq experiment
rnaseqpower sspa sample size sequencing complex-design
updated 8.8 years ago by ▴ 20 • written 8.8 years ago by • 0
0
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4
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1.7k
views
IONiseR readFast5Summary Error
R sequencing preprocessing bioconductor
updated 8.9 years ago by ★ 6.6k • written 9.0 years ago by • 0
1
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0
replies
1.9k
views
Job: Post-doc Position in Epigenetic Bioinformatics
cancer sequencing epigenetics computational biology bioinformatics Job
9.0 years ago Yassen Assenov ▴ 10
1
vote
1
reply
2.6k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing biostrings shortread
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 10
1
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2
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2.4k
views
DNAcopy: Using log-ratios and B-allele frequencies
sequencing snp
updated 9.2 years ago by ▴ 20 • written 9.2 years ago by • 0
1
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2
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1.5k
views
Can I use rtracklayer to get the sequence surrounding a set of variants?
rtracklayer sequencing reference genome
9.2 years ago Stephanie M. Gogarten ▴ 870
1
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1
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2.3k
views
Perplexing results with Limma with RNA-seq data
sequencing microarray
updated 9.3 years ago by ★ 13k • written 9.3 years ago by ▴ 420
3
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0
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1.9k
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News: BioCAsia, 8 Sept 2015, Tokyo
sequencing transcription epigenomics visualization infrastructure News
9.4 years ago • updated 9.3 years ago Matthew Ritchie ▴ 1000
0
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2
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1.9k
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preparing sequencing data for use with anota
Sequencing Normalization PROcess anota Sequencing Normalization PROcess anota
updated 9.3 years ago by • 0 • written 10.7 years ago by ★ 13k
3
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1
reply
2.4k
views
Adjusting for gender using limma
limma microarray sequencing
updated 9.3 years ago by 67k • written 9.3 years ago by ▴ 420
0
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1
reply
1.6k
views
Getting data on the out-of-frame transcripts
annotate sequencing genomicfeatures
updated 9.3 years ago by 16k • written 9.3 years ago by • 0
3
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4
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3.8k
views
Variance filtering prior to RNA-seq differential expression
sequencing deseq limma
updated 9.3 years ago by 51k • written 9.3 years ago by ▴ 420
0
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2
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4.0k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 9.4 years ago by • 0 • written 11.6 years ago by ★ 8.2k
4
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2
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2.5k
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Detect global differences in miRNA expression between tumor and normal using spike-ins
edger limma mirna sequencing
updated 9.4 years ago by ★ 28k • written 9.4 years ago by ▴ 40
2
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3
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1.9k
views
SVA batch effects for different technologies
normalization deseq2 sequencing sva
9.4 years ago marcin.bazyliszek • 0
4
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0
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1.6k
views
News: Hands-on Bioconductor course, 7 Sept 2015, Tokyo
sequencing transcription variantfiltering annotation News
9.4 years ago Matthew Ritchie ▴ 1000
2
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4
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7.4k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing Alignment DESeq DESeq2 Sequencing Alignment DESeq DESeq2
updated 9.5 years ago by • 0 • written 10.5 years ago by ★ 13k
50 results • Page 1 of 1
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Answer: Downloading Metagenomic Data with Higher Taxonomic Units by Levi Waldron ★ 1.1k
I'm sorry I missed the first post! Yes, it is easy to agglomerate ranks in curatedMetagenomicData datasets. See the example in the vignette…
Comment: Differene between the Wald and LRT test for time-series gene expression data by Denise • 0
This makes a lot of sense, thank you very much!
Comment: Downloading Metagenomic Data with Higher Taxonomic Units by elozanoe • 0
Hi! I'm facing the same problem. Is there any easy way to output relative abundances of higher taxonomic units (up to kingdom), similar to…
Comment: Is it recommended to analyze different tissues together when using edgeR by Gordon Smyth 51k
Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
Comment: Handling Epic Array Data by Melisa Tecik • 0
Thanks a lot for the help. You saved my day
Votes
A: Error in DESeqDataSet : some values in assay are not integers
A: correcting the batch effects in Limma and SVA
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
Answer: Differene between the Wald and LRT test for time-series gene expression data
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