Showing : sequencing • reset
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Job: Tenure-track Group Leader Positions in Computational Biology and Biological Chemistry
bioinformatics genomics proteomics biologicalchemistry sequencing
3 months ago Robert Castelo ★ 2.8k
6
votes
6
replies
377
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Batch effect from to sequencing data at differents depths
Sequencing sequencingDeepth BatchEffect DESeq2
6 months ago ary.lech ▴ 10
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0
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232
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Job: Bioinformatician position at University of Texas Southwestern Medical Center
Sequencing bioinformatics
6 months ago chao.xing • 0
1
vote
3
replies
345
views
Preferential sequencing of longer Genes in Illumina?
DESeq2 sequencing
updated 14 months ago by • 0 • written 14 months ago by • 0
2
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2
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339
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is the P value reliable if the counts are Low across the sample ?
DESeq2 sequencing
14 months ago simplyphage • 0
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0
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430
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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
16 months ago • updated 15 months ago lhd • 0
0
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0
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370
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Job: Tenure-track Group Leader Position in Computational Biology
bioinformatics sequencing barcelona proteomics
15 months ago Robert Castelo ★ 2.8k
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0
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342
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Job: Scientist/Senior Scientist, Statistical Geneticist
Sequencing Genetics GeneticsPed statistics
16 months ago António Miguel de Jesus Domingues ▴ 480
0
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0
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343
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Job: Postdoc: BIOINFORMATICS FOR FUNCTIONAL GENOMICS AND POPULATION GENETICS OF CANCER
GWAS lung cancer functional genomics eQTL sequencing Job
2.1 years ago jiyeon.choi2 • 0
0
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0
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352
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Job: Post-doc fellow - Aparicio Lab
single cell bioinformatics genome sequencing Job
2.7 years ago jmaanaki • 0
0
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2
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518
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DESeq2 error on analyzing microbiome data
deseq2 microbiome sequencing
2.9 years ago zhigang.li • 0
2
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3
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673
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Boxplot function not showing all reads length on x-axis
boxplot reads fastq sequencing rsubread
updated 3.0 years ago by ★ 3.4k • written 3.0 years ago by ▴ 60
0
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1
reply
405
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Annotating protein sequences
Protein iranges sequencing
3.2 years ago ieuangw • 0
0
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0
replies
1.4k
views
Job: Postdoc in Population Genomics - UC Davis
bioinformatics evolution sequencing genome analysis genomics Job
3.6 years ago hschmidt • 0
0
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0
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532
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Job: Research Associate- Production Bioinformatics - Atlantic Cancer Research Institute - Moncton -New Brunwsiwck - Canada
cancer bioinformatics bioinformatician job sequencing Job
3.8 years ago gabriel.wajnberg • 0
1
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10
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1.2k
views
Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
deseq2 sequencing ribosome profiling riboseq multiple factor design
updated 3.8 years ago by 37k • written 3.8 years ago by ▴ 10
0
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0
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620
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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
3.9 years ago Andy Lynch ▴ 100
0
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0
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391
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Number of reads needed for Guide-Seq
sequencing
4.1 years ago Jacques-P.Tremblay • 0
1
vote
1
reply
1.3k
views
Rsamtools : separating mapped and unmapped reads from BAM or SAM files (for a newbie)
R sequencing alignment rsamtools mapping
updated 4.1 years ago by 59k • written 4.1 years ago by ▴ 10
0
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0
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497
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Sequence composition effect
sequencing rnaseq_analysis
4.3 years ago alemutak • 0
0
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1
reply
775
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write ab1 files
sangerseqr sequencing abi
4.7 years ago tmolosh • 0
2
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11
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1.2k
views
DESeq2 polysome profiling analysis with 2 interaction terms
deseq2 sequencing polysome profiling
updated 5.0 years ago by 37k • written 5.0 years ago by ▴ 10
0
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0
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1.2k
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
5.7 years ago dtlabmskcc • 0
3
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8
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3.2k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing DESeq Sequencing DESeq
updated 5.7 years ago by • 0 • written 8.4 years ago by ★ 12k
0
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7
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1.4k
views
Bioconductor 2.6 is released
Sequencing Microarray Visualization Infrastructure PROcess beadarray keggorthology eisa
updated 5.7 years ago by • 0 • written 12.1 years ago by 1.6k
8
votes
2
replies
2.3k
views
Appropriate ways to filter counts data for voom/limma
limma edger sequencing
updated 5.8 years ago by 45k • written 5.8 years ago by ▴ 10
6
votes
4
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798
views
How to normalize chemical genomics barcode sequencing data
limma normalization sequencing edger
updated 5.9 years ago by ★ 27k • written 5.9 years ago by ▴ 20
0
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4
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1.8k
views
DNAString: Standard checksum function?
Biostrings FASTA sequencing
6.2 years ago Henrik Bengtsson ★ 2.4k
2
votes
4
replies
997
views
Complex ANOVA analysis in EdgeR
edger anova sequencing
updated 6.2 years ago by ★ 27k • written 6.2 years ago by • 0
0
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5
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1.3k
views
getting sample size for RNAseq experiment
rnaseqpower sspa sample size sequencing complex-design
updated 6.3 years ago by ▴ 20 • written 6.3 years ago by • 0
0
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4
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1.1k
views
IONiseR readFast5Summary Error
R sequencing preprocessing bioconductor
updated 6.4 years ago by ★ 5.5k • written 6.5 years ago by • 0
1
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0
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1.3k
views
Job: Post-doc Position in Epigenetic Bioinformatics
cancer sequencing epigenetics computational biology bioinformatics Job
6.5 years ago Yassen Assenov ▴ 10
1
vote
1
reply
1.9k
views
Trim DNAStringSets using ShortRead while keeping the primer sequences?
sequencing biostrings shortread
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 10
1
vote
2
replies
1.4k
views
DNAcopy: Using log-ratios and B-allele frequencies
sequencing snp
updated 6.6 years ago by ▴ 20 • written 6.6 years ago by • 0
1
vote
2
replies
824
views
Can I use rtracklayer to get the sequence surrounding a set of variants?
rtracklayer sequencing reference genome
6.7 years ago Stephanie M. Gogarten ▴ 820
1
vote
1
reply
1.8k
views
Perplexing results with Limma with RNA-seq data
sequencing microarray
updated 6.8 years ago by 13k • written 6.8 years ago by ▴ 400
3
votes
0
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1.2k
views
News: BioCAsia, 8 Sept 2015, Tokyo
sequencing transcription epigenomics visualization infrastructure News
6.9 years ago • updated 6.8 years ago Matthew Ritchie ▴ 1000
0
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2
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1.2k
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preparing sequencing data for use with anota
Sequencing Normalization PROcess anota Sequencing Normalization PROcess anota
updated 6.8 years ago by • 0 • written 8.2 years ago by ★ 12k
3
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1
reply
1.7k
views
Adjusting for gender using limma
limma microarray sequencing
updated 6.8 years ago by 59k • written 6.8 years ago by ▴ 400
0
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1
reply
1.0k
views
Getting data on the out-of-frame transcripts
annotate sequencing genomicfeatures
updated 6.8 years ago by 15k • written 6.8 years ago by • 0
3
votes
4
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2.5k
views
Variance filtering prior to RNA-seq differential expression
sequencing deseq limma
updated 6.8 years ago by 45k • written 6.8 years ago by ▴ 400
0
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2
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2.9k
views
Bioconductor 2.12 is released
BiocViews aCGH SNP Transcription Sequencing Microarray Coverage Alignment Annotation GO
updated 6.9 years ago by • 0 • written 9.1 years ago by ★ 8.2k
4
votes
2
replies
1.6k
views
Detect global differences in miRNA expression between tumor and normal using spike-ins
edger limma mirna sequencing
updated 6.9 years ago by ★ 27k • written 6.9 years ago by ▴ 40
2
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3
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1.2k
views
SVA batch effects for different technologies
normalization deseq2 sequencing sva
6.9 years ago marcin.bazyliszek • 0
4
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0
replies
1.1k
views
News: Hands-on Bioconductor course, 7 Sept 2015, Tokyo
sequencing transcription variantfiltering annotation News
6.9 years ago Matthew Ritchie ▴ 1000
2
votes
4
replies
5.1k
views
DESeq2 Error in estimateSizeFactorsForMatrix
Sequencing Alignment DESeq DESeq2 Sequencing Alignment DESeq DESeq2
updated 7.0 years ago by • 0 • written 8.0 years ago by ★ 12k
0
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0
replies
1.3k
views
Job: Bioinformatics Scientist, Astex Pharmaceuticals
bioinformatician job oncology sequencing drug development Job
7.0 years ago Harpreet Saini ▴ 30
1
vote
0
replies
919
views
Genome editing analysis with Illumina sequencing
indel sequencing alignment
7.1 years ago Merienne Nicolas ▴ 120
0
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0
replies
657
views
Invitation Research Collaborations
cancer microarray mirna sequencing
7.1 years ago alexandru.floares • 0
0
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0
replies
1.2k
views
Job: Research Associate, Cambridge, UK - Oesophageal Cancer ICGC project
job sequencing methylation expression Job
7.3 years ago Andy Lynch ▴ 100
50 results • Page 1 of 1
Recent ...
Replies
Comment: ashr vs apeglm for interaction data by Ali Barry ▴ 30
Thanks, I'll trying playing a bit there. I have done some minor filtering already (requiring at least 5 counts in 10% of my samples, across…
Comment: ashr vs apeglm for interaction data by Michael Love 37k
I see why apeglm is conservative— the dispersion is very high within group. An idea would be to use ashr but do some additional filtering …
Comment: How to figure out the FC value from Limma by ATpoint ★ 1.2k
That’s an Excel problem, not a GEO/R problem or related to limma and Bioconductor.
Comment: ashr vs apeglm for interaction data by Ali Barry ▴ 30
Hi Michael, Plots attached. Many of the large fold changes with `ashr` are driven by one sample per group, but a few are maybe a bit more …
Comment: regression analysis for epic array methylation data using limma by nabiyogesh ▴ 10
Thanks! I have tried this; I am not sure after that how to find logeGFR associated probe? and also, how to filter significant probe? …
Votes
Answer: How to properly use DESeq2 for an experiment
Comment: ashr vs apeglm for interaction data
Comment: How to figure out the FC value from Limma
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
Awards • All
Popular Question to Gordon Smyth 45k
Popular Question to Robert Castelo ★ 2.8k
Popular Question to andrebolerbarros ▴ 10
Scholar to James W. MacDonald 59k
Scholar to Guido Hooiveld ★ 3.2k
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