Showing : Transcriptomics • reset
3
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236
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
7 weeks ago Anita ▴ 10
3
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5
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1.4k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 10 months ago by 42k • written 10 months ago by • 0
0
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4
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758
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problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
12 months ago sreeshmaraj72 • 0
0
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1
reply
364
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Time change in expression vs time change in phenotype
Transcriptomics ExpressionData DESeq2
updated 13 months ago by 42k • written 13 months ago by • 0
4
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5
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1.8k
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EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
Transcriptomics EnhancedVolcano
updated 13 months ago by ★ 3.9k • written 13 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 13 months ago by ★ 13k • written 13 months ago by ▴ 20
0
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3
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762
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 14 months ago by 50k • written 15 months ago by • 0
0
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1
reply
748
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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 16 months ago by ★ 1.5k • written 16 months ago by ▴ 10
0
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1
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1.3k
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Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 16 months ago by 42k • written 16 months ago by • 0
0
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0
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548
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EdgeR without replication
Transcriptomics
17 months ago kuttibiotech2009 • 0
0
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559
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Analysis of TIF-seq data to generate transcription start sites (TSS) and poly(A) site (PAS) clusters
Transcriptomics SequencingData
18 months ago Rom • 0
0
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0
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634
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Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
18 months ago whduke • 0
0
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2
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697
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Questions about `collapseReplicates` function in DESeq2
DESeq2 Transcriptomics
19 months ago Yijing • 0
0
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0
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536
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
20 months ago Julieta • 0
2
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1
reply
1.6k
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Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 20 months ago by ★ 4.1k • written 20 months ago by ▴ 10
0
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3
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1000
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DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics DESeq2
22 months ago marius.wenzel • 0
4
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6
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1.4k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
2.0 years ago • updated 24 months ago mohammedtoufiq91 ▴ 10
1
vote
3
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1.1k
views
Identifying DEG between development stages
plant Transcriptomics DESeq2 r
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
2
votes
5
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1.4k
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DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 2.2 years ago by 42k • written 2.2 years ago by • 0
2
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2
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839
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Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
2.6 years ago • updated 12 months ago diangomaiga • 0
1
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2
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1.3k
views
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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927
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.8 years ago lianov • 0
0
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0
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851
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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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976
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db Transcriptomics
3.1 years ago Kate • 0
0
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0
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943
views
Consensus wgcna soft threshold for each data
Transcriptomics WGCNA wgcna
3.2 years ago 2323982403 ▴ 60
0
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1
reply
776
views
Metatranscriptomics DESeq2 multifactorial sampling
Transcriptomics DESeq2
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
0
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0
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955
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Job: Bioinformatician at MiroBio, Oxford, UK
Transcriptomics Bioconductor Statistics Job Biocon
3.2 years ago m.jackson • 0
5
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5
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2.5k
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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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949
views
Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
3.4 years ago Steve Lianoglou ★ 13k
1
vote
1
reply
918
views
NanoStringDiff Not Recognized as Numeric
Bioconductor Transcriptomics NanoStringDiff
updated 3.6 years ago by 1.6k • written 3.6 years ago by ▴ 10
0
votes
0
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703
views
Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
4.1 years ago raquelponti • 0
1
vote
0
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983
views
News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
4.3 years ago Laurent Gatto 1.6k
0
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4
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1.1k
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 4.3 years ago by ▴ 350 • written 4.3 years ago by • 0
0
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0
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895
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Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
4.4 years ago Joseph Barry ▴ 10
0
votes
0
replies
773
views
Job: Bionformatician in personalized oncotherapy (BEL)
job bioinformatician immunotherapy genomics transcriptomics Job
4.5 years ago cedric • 0
1
vote
0
replies
873
views
Job: Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics gene expression time series plant biology circadian Job
4.6 years ago dezer ▴ 10
2
votes
2
replies
2.9k
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
votes
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
vote
1
reply
935
views
cpm filtering parameter
cpm filtering transcriptomics rnaseq edgeR metatranscriptomics
updated 4.7 years ago by 50k • written 4.7 years ago by ▴ 10
0
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0
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792
views
How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r metabolomics KEGG Proteomics Transcriptomics
5.1 years ago Wuschel ▴ 10
0
votes
0
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935
views
Job: Bionformatician Position / Heidelberg
neuroscience data integration transcriptomics Job
5.1 years ago slezak • 0
1
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0
replies
1.6k
views
Job: Full time and permanent research logistician in Bioinformatics
transcriptomics proteomics job bioinformatician Job
5.2 years ago Laurent Gatto 1.6k
1
vote
1
reply
1.4k
views
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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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 5.6 years ago by ▴ 80 • written 5.6 years ago by • 0
44 results • Page 1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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