Showing : Transcriptomics • reset
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
19 days ago • updated 16 days ago sindhuri • 0
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117
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Filtering Steps for proActiv Analysis
Transcriptomics proActiv
3 months ago LuciaNhu • 0
1
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6
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787
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 3 months ago by ★ 4.6k • written 4 months ago by • 0
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0
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265
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proActiv-promoter analysis
proActiv Transcriptomics
5 months ago wang.xiangyu • 0
0
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0
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405
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Job: Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell Transcriptomics SpatialDatasets SpatialData
8 months ago Silvio • 0
3
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2
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522
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
10 months ago Anita ▴ 10
4
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5
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2.7k
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DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 18 months ago by 43k • written 19 months ago by • 0
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4
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1.1k
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
20 months ago sreeshmaraj72 • 0
0
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1
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536
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Time change in expression vs time change in phenotype
Transcriptomics ExpressionData DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
4
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5
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2.8k
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EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
Transcriptomics EnhancedVolcano
updated 21 months ago by ★ 4.0k • written 21 months ago by ▴ 20
4
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8
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1.9k
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DESEQ2 - What is the recommended workflow in terms of pre-filtering and counts normalization?
DESeq2 Transcriptomics
updated 21 months ago by ★ 13k • written 22 months ago by ▴ 20
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3
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1.1k
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 23 months ago by 52k • written 23 months ago by • 0
0
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1
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1.0k
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Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.0 years ago by ★ 1.5k • written 2.0 years ago by ▴ 10
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1
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2.1k
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Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 2.0 years ago by 43k • written 2.1 years ago by • 0
0
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Analysis of TIF-seq data to generate transcription start sites (TSS) and poly(A) site (PAS) clusters
Transcriptomics SequencingData
2.2 years ago Rom • 0
0
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866
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Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
2.2 years ago whduke • 0
0
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2
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899
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Questions about `collapseReplicates` function in DESeq2
DESeq2 Transcriptomics
2.3 years ago Yijing • 0
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0
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724
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
2.4 years ago Julieta • 0
3
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1
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2.8k
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Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.4 years ago by ★ 4.6k • written 2.4 years ago by ▴ 10
0
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3
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1.4k
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DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics DESeq2
2.5 years ago marius.wenzel • 0
4
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6
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1.8k
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How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
2.7 years ago mohammedtoufiq91 ▴ 10
1
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3
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1.5k
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Identifying DEG between development stages
plant Transcriptomics DESeq2 r
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
2
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5
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1.7k
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DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
2
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2
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1.1k
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
3.3 years ago • updated 20 months ago diangomaiga • 0
1
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2
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1.6k
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Not many DE genes using glmTreat
EdgeR Bioinformatics Transcriptomics Quantseq
3.4 years ago Barista • 0
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1.1k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.5 years ago lianov • 0
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1.0k
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Job: [apply by 8/15] PhD scholarship on functional and evolutionary genomics
JobPosting Transcriptomics GenomicVariation
3.5 years ago marie • 0
0
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2
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1.4k
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Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db Transcriptomics
3.8 years ago Kate • 0
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0
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1.1k
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Consensus wgcna soft threshold for each data
Transcriptomics WGCNA wgcna
3.9 years ago 2323982403 ▴ 60
0
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1
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968
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Metatranscriptomics DESeq2 multifactorial sampling
Transcriptomics DESeq2
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
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1.1k
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Job: Bioinformatician at MiroBio, Oxford, UK
Transcriptomics Bioconductor Statistics Job Biocon
3.9 years ago m.jackson • 0
5
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5
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3.3k
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analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 3.9 years ago by 67k • written 3.9 years ago by ▴ 10
0
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0
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1.2k
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
4.1 years ago Steve Lianoglou ★ 13k
1
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1
reply
1.1k
views
NanoStringDiff Not Recognized as Numeric
Bioconductor Transcriptomics NanoStringDiff
updated 4.3 years ago by 1.6k • written 4.3 years ago by ▴ 10
0
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0
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878
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
4.8 years ago raquelponti • 0
1
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0
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1.2k
views
News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
5.0 years ago Laurent Gatto 1.6k
0
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4
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1.3k
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 5.0 years ago by ▴ 350 • written 5.0 years ago by • 0
0
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1.1k
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Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
5.1 years ago Joseph Barry ▴ 10
0
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0
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923
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Job: Bionformatician in personalized oncotherapy (BEL)
job bioinformatician immunotherapy genomics transcriptomics Job
5.2 years ago cedric • 0
1
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1.1k
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Job: Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics gene expression time series plant biology circadian Job
5.3 years ago dezer ▴ 10
2
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2
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3.8k
views
How adjusted p-values are calculated in limma
limma r transcriptomics FDR statistics
updated 5.3 years ago by 52k • written 5.3 years ago by ▴ 10
2
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0
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2.5k
views
Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics genomics transcriptomics software Job
5.3 years ago Laurent Gatto 1.6k
1
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1
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1.2k
views
cpm filtering parameter
cpm filtering transcriptomics rnaseq edgeR metatranscriptomics
updated 5.4 years ago by 52k • written 5.4 years ago by ▴ 10
0
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1.1k
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Job: Bionformatician Position / Heidelberg
neuroscience data integration transcriptomics Job
5.8 years ago slezak • 0
0
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0
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971
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How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r metabolomics KEGG Proteomics Transcriptomics
5.8 years ago Wuschel ▴ 10
1
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0
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1.8k
views
Job: Full time and permanent research logistician in Bioinformatics
transcriptomics proteomics job bioinformatician Job
5.9 years ago • updated 5.8 years ago Laurent Gatto 1.6k
1
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1
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1.6k
views
News: Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq deseq2 proteomics transcriptomics workshop News
written 5.9 years ago by 1.6k
3
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4
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1.6k
views
Writing a loop to clean up protein names
Proteomics Transcriptomics Loops batch-processing R
updated 6.3 years ago by ▴ 80 • written 6.3 years ago by • 0
48 results • Page 1 of 1
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Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k
I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…
Comment: Csaw normalization strategies - general inquiry by Luca • 0
Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10
Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …
Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k
My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …
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Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
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