Showing : transcriptomics • reset
2
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4
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2.7k
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Altered (negative or positive) logFC values for same gene from two intitial count matrices, one being a subset of the other
Transcriptomics edgeR DEG
7 months ago Maziya • 0
0
votes
3
replies
1.0k
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 12 months ago by • 0
0
votes
0
replies
320
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Filtering Steps for proActiv Analysis
Transcriptomics proActiv
14 months ago LuciaNhu • 0
1
vote
6
replies
2.0k
views
New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
0
votes
0
replies
487
views
proActiv-promoter analysis
proActiv Transcriptomics
17 months ago wang.xiangyu • 0
0
votes
0
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878
views
Job: Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell Transcriptomics SpatialDatasets SpatialData
19 months ago Silvio • 0
3
votes
2
replies
815
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
22 months ago Anita ▴ 10
4
votes
5
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4.1k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
0
votes
4
replies
1.4k
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
2.7 years ago sreeshmaraj72 • 0
0
votes
1
reply
763
views
Time change in expression vs time change in phenotype
Transcriptomics ExpressionData DESeq2
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
4
votes
5
replies
3.8k
views
EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
Transcriptomics EnhancedVolcano
updated 2.8 years ago by ★ 4.0k • written 2.8 years ago by ▴ 20
4
votes
8
replies
3.1k
views
DESEQ2 - What is the recommended workflow in terms of pre-filtering and counts normalization?
DESeq2 Transcriptomics
updated 2.8 years ago by ★ 13k • written 2.8 years ago by ▴ 20
0
votes
3
replies
1.5k
views
Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
votes
1
reply
1.3k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 3.0 years ago by ★ 1.6k • written 3.0 years ago by ▴ 10
0
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1
reply
3.1k
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
0
votes
0
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1.0k
views
Analysis of TIF-seq data to generate transcription start sites (TSS) and poly(A) site (PAS) clusters
Transcriptomics SequencingData
3.2 years ago Rom • 0
0
votes
0
replies
1.1k
views
Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
3.2 years ago whduke • 0
0
votes
2
replies
1.1k
views
Questions about `collapseReplicates` function in DESeq2
DESeq2 Transcriptomics
3.2 years ago Yijing • 0
0
votes
0
replies
1.3k
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
3.3 years ago Julieta • 0
3
votes
1
reply
4.3k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by ▴ 10
0
votes
3
replies
1.8k
views
DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics DESeq2
3.5 years ago marius.wenzel • 0
4
votes
6
replies
2.4k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
3.7 years ago mohammedtoufiq91 ▴ 10
1
vote
3
replies
1.9k
views
Identifying DEG between development stages
plant Transcriptomics DESeq2 r
updated 3.8 years ago by ▴ 780 • written 3.8 years ago by • 0
2
votes
5
replies
2.0k
views
DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
2
votes
2
replies
1.4k
views
Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
4.3 years ago • updated 2.7 years ago diangomaiga • 0
1
vote
2
replies
2.1k
views
Not many DE genes using glmTreat
EdgeR Bioinformatics Transcriptomics Quantseq
4.4 years ago Barista • 0
0
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0
replies
1.4k
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
4.5 years ago lianov • 0
0
votes
0
replies
1.3k
views
Job: [apply by 8/15] PhD scholarship on functional and evolutionary genomics
JobPosting Transcriptomics GenomicVariation
4.5 years ago marie • 0
0
votes
2
replies
2.0k
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db Transcriptomics
4.8 years ago Kate • 0
0
votes
0
replies
1.4k
views
Consensus wgcna soft threshold for each data
Transcriptomics WGCNA wgcna
4.8 years ago 2323982403 ▴ 60
0
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1
reply
1.2k
views
Metatranscriptomics DESeq2 multifactorial sampling
Transcriptomics DESeq2
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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0
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1.5k
views
Job: Bioinformatician at MiroBio, Oxford, UK
Transcriptomics Bioconductor Statistics Job Biocon
4.9 years ago m.jackson • 0
5
votes
5
replies
5.3k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 4.9 years ago by 68k • written 4.9 years ago by ▴ 10
0
votes
0
replies
1.5k
views
Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
5.1 years ago Steve Lianoglou ★ 13k
1
vote
1
reply
1.4k
views
NanoStringDiff Not Recognized as Numeric
Bioconductor Transcriptomics NanoStringDiff
updated 5.2 years ago by 1.6k • written 5.2 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
5.8 years ago raquelponti • 0
1
vote
0
replies
1.5k
views
News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
5.9 years ago Laurent Gatto 1.6k
0
votes
4
replies
1.7k
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 6.0 years ago by ▴ 350 • written 6.0 years ago by • 0
0
votes
0
replies
1.4k
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Job: Bioinformatics Scientist, CNS Transcriptomics at Alnylam Pharmaceuticals, Cambridge MA, USA
scRNA-seq CNS transcriptomics RNAi Job
6.0 years ago Joseph Barry ▴ 10
0
votes
0
replies
1.1k
views
Job: Bionformatician in personalized oncotherapy (BEL)
job bioinformatician immunotherapy genomics transcriptomics Job
6.1 years ago cedric • 0
1
vote
0
replies
1.3k
views
Job: Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics gene expression time series plant biology circadian Job
6.3 years ago dezer ▴ 10
2
votes
2
replies
4.6k
views
How adjusted p-values are calculated in limma
limma r transcriptomics FDR statistics
updated 6.3 years ago by 53k • written 6.3 years ago by ▴ 10
2
votes
0
replies
2.8k
views
Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics genomics transcriptomics software Job
6.3 years ago Laurent Gatto 1.6k
1
vote
1
reply
1.5k
views
cpm filtering parameter
cpm filtering transcriptomics rnaseq edgeR metatranscriptomics
updated 6.3 years ago by 53k • written 6.3 years ago by ▴ 10
0
votes
0
replies
1.4k
views
Job: Bionformatician Position / Heidelberg
neuroscience data integration transcriptomics Job
6.8 years ago slezak • 0
0
votes
0
replies
1.2k
views
How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r metabolomics KEGG Proteomics Transcriptomics
6.8 years ago Wuschel ▴ 10
1
vote
0
replies
2.0k
views
Job: Full time and permanent research logistician in Bioinformatics
transcriptomics proteomics job bioinformatician Job
6.9 years ago • updated 6.8 years ago Laurent Gatto 1.6k
1
vote
1
reply
1.9k
views
News: Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq deseq2 proteomics transcriptomics workshop News
written 6.9 years ago by 1.6k
3
votes
4
replies
2.0k
views
Writing a loop to clean up protein names
Proteomics Transcriptomics Loops batch-processing R
updated 7.3 years ago by ▴ 80 • written 7.3 years ago by • 0
49 results • Page 1 of 1
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Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
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