Showing : transcriptomics • reset
3
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
29 days ago Anita ▴ 10
1
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1
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1.4k
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News: Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq deseq2 proteomics transcriptomics workshop News
written 5.2 years ago by 1.6k
3
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5
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1.3k
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DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 9 months ago by 41k • written 9 months ago by • 0
0
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4
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730
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
2
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2
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806
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
2.5 years ago • updated 11 months ago diangomaiga • 0
0
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1
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341
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Time change in expression vs time change in phenotype
Transcriptomics ExpressionData DESeq2
updated 12 months ago by 41k • written 12 months ago by • 0
4
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5
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1.6k
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EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
Transcriptomics EnhancedVolcano
updated 12 months ago by ★ 3.9k • written 12 months ago by ▴ 20
4
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8
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1.3k
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DESEQ2 - What is the recommended workflow in terms of pre-filtering and counts normalization?
DESeq2 Transcriptomics
updated 12 months ago by ★ 13k • written 12 months ago by ▴ 20
0
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3
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730
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 14 months ago by 50k • written 14 months ago by • 0
0
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1
reply
710
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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 15 months ago by ★ 1.5k • written 15 months ago by ▴ 10
0
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1
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1.2k
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Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 15 months ago by 41k • written 15 months ago by • 0
0
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520
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EdgeR without replication
Transcriptomics
16 months ago kuttibiotech2009 • 0
0
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542
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Analysis of TIF-seq data to generate transcription start sites (TSS) and poly(A) site (PAS) clusters
Transcriptomics SequencingData
17 months ago Rom • 0
0
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0
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588
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Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
17 months ago whduke • 0
0
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2
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680
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Questions about `collapseReplicates` function in DESeq2
DESeq2 Transcriptomics
18 months ago Yijing • 0
0
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0
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514
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
19 months ago Julieta • 0
2
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1
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1.5k
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Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 19 months ago by ★ 4.0k • written 19 months ago by ▴ 10
0
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3
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959
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DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics DESeq2
21 months ago marius.wenzel • 0
4
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6
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1.4k
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How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
23 months ago mohammedtoufiq91 ▴ 10
1
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3
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1.0k
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Identifying DEG between development stages
plant Transcriptomics DESeq2 r
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
2
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5
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1.4k
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DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
1
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2
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1.3k
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Not many DE genes using glmTreat
EdgeR Bioinformatics Transcriptomics Quantseq
2.7 years ago Barista • 0
0
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0
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896
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.7 years ago lianov • 0
0
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0
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813
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Job: [apply by 8/15] PhD scholarship on functional and evolutionary genomics
JobPosting Transcriptomics GenomicVariation
2.8 years ago marie • 0
0
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2
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942
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Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db Transcriptomics
3.0 years ago Kate • 0
0
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0
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922
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Consensus wgcna soft threshold for each data
Transcriptomics WGCNA wgcna
3.1 years ago 2323982403 ▴ 60
0
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1
reply
753
views
Metatranscriptomics DESeq2 multifactorial sampling
Transcriptomics DESeq2
updated 3.1 years ago by 41k • written 3.1 years ago by • 0
0
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0
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934
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Job: Bioinformatician at MiroBio, Oxford, UK
Transcriptomics Bioconductor Statistics Job Biocon
3.1 years ago m.jackson • 0
5
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5
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2.4k
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analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 10
0
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0
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923
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Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.3 years ago Steve Lianoglou ★ 13k
1
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1
reply
892
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NanoStringDiff Not Recognized as Numeric
Bioconductor Transcriptomics NanoStringDiff
updated 3.5 years ago by 1.6k • written 3.5 years ago by ▴ 10
0
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0
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688
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
4.1 years ago raquelponti • 0
1
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0
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951
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News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
4.2 years ago Laurent Gatto 1.6k
0
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4
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1.0k
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 4.2 years ago by ▴ 350 • written 4.2 years ago by • 0
0
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0
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863
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Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
4.3 years ago Joseph Barry ▴ 10
0
votes
0
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762
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Job: Bionformatician in personalized oncotherapy (BEL)
job bioinformatician immunotherapy genomics transcriptomics Job
4.4 years ago cedric • 0
1
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0
replies
856
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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
4.5 years ago dezer ▴ 10
2
votes
2
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2.8k
views
How adjusted p-values are calculated in limma
limma r transcriptomics FDR statistics
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 10
2
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0
replies
2.3k
views
Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics genomics transcriptomics software Job
4.6 years ago Laurent Gatto 1.6k
1
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1
reply
912
views
cpm filtering parameter
cpm filtering transcriptomics rnaseq edgeR metatranscriptomics
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 10
0
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0
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921
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Job: Bionformatician Position / Heidelberg
neuroscience data integration transcriptomics Job
5.1 years ago • updated 5.0 years ago slezak • 0
0
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0
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773
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How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r metabolomics KEGG Proteomics Transcriptomics
5.1 years ago Wuschel ▴ 10
1
vote
0
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1.6k
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Job: Full time and permanent research logistician in Bioinformatics
transcriptomics proteomics job bioinformatician Job
5.2 years ago • updated 5.1 years ago Laurent Gatto 1.6k
3
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4
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1.3k
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Writing a loop to clean up protein names
Proteomics Transcriptomics Loops batch-processing R
updated 5.5 years ago by ▴ 80 • written 5.5 years ago by • 0
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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