Showing : transcriptomics • reset
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 6 weeks ago by • 0
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0
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134
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Filtering Steps for proActiv Analysis
Transcriptomics proActiv
3 months ago LuciaNhu • 0
1
vote
6
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892
views
New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 4 months ago by ★ 4.7k • written 5 months ago by • 0
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0
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281
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proActiv-promoter analysis
proActiv Transcriptomics
6 months ago wang.xiangyu • 0
0
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0
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437
views
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
votes
2
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539
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How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
11 months ago Anita ▴ 10
4
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5
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2.8k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
0
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4
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1.1k
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
21 months ago sreeshmaraj72 • 0
0
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1
reply
552
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Time change in expression vs time change in phenotype
Transcriptomics ExpressionData DESeq2
updated 22 months ago by 43k • written 22 months ago by • 0
4
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5
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2.9k
views
EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
Transcriptomics EnhancedVolcano
updated 22 months ago by ★ 4.0k • written 22 months ago by ▴ 20
4
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8
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2.0k
views
DESEQ2 - What is the recommended workflow in terms of pre-filtering and counts normalization?
DESeq2 Transcriptomics
updated 22 months ago by ★ 13k • written 22 months ago by ▴ 20
0
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3
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1.1k
views
Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 24 months ago by 52k • written 24 months ago by • 0
0
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1
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1.0k
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 2.1 years ago by ★ 1.6k • written 2.1 years ago by ▴ 10
0
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1
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2.3k
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Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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0
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795
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Analysis of TIF-seq data to generate transcription start sites (TSS) and poly(A) site (PAS) clusters
Transcriptomics SequencingData
2.3 years ago Rom • 0
0
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0
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881
views
Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
2.3 years ago whduke • 0
0
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2
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918
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Questions about `collapseReplicates` function in DESeq2
DESeq2 Transcriptomics
2.3 years ago Yijing • 0
0
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0
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734
views
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
votes
1
reply
2.9k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.4 years ago by ★ 4.7k • written 2.4 years ago by ▴ 10
0
votes
3
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1.5k
views
DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics DESeq2
2.6 years ago marius.wenzel • 0
4
votes
6
replies
1.9k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
2.8 years ago mohammedtoufiq91 ▴ 10
1
vote
3
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1.5k
views
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
views
DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
2
votes
2
replies
1.1k
views
Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
3.4 years ago • updated 21 months ago diangomaiga • 0
1
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2
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1.7k
views
Not many DE genes using glmTreat
EdgeR Bioinformatics Transcriptomics Quantseq
3.5 years ago Barista • 0
0
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0
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1.2k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.6 years ago lianov • 0
0
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0
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1.0k
views
Job: [apply by 8/15] PhD scholarship on functional and evolutionary genomics
JobPosting Transcriptomics GenomicVariation
3.6 years ago marie • 0
0
votes
2
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1.5k
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db Transcriptomics
3.9 years ago Kate • 0
0
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0
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1.2k
views
Consensus wgcna soft threshold for each data
Transcriptomics WGCNA wgcna
3.9 years ago 2323982403 ▴ 60
0
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1
reply
989
views
Metatranscriptomics DESeq2 multifactorial sampling
Transcriptomics DESeq2
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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0
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1.2k
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Job: Bioinformatician at MiroBio, Oxford, UK
Transcriptomics Bioconductor Statistics Job Biocon
4.0 years ago m.jackson • 0
5
votes
5
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3.5k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 4.0 years ago by 68k • written 4.0 years ago by ▴ 10
0
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0
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1.3k
views
Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
4.2 years ago Steve Lianoglou ★ 13k
1
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1
reply
1.2k
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
votes
0
replies
903
views
Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
4.9 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 5.1 years ago by ▴ 350 • written 5.1 years ago by • 0
0
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0
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1.1k
views
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
replies
936
views
Job: Bionformatician in personalized oncotherapy (BEL)
job bioinformatician immunotherapy genomics transcriptomics Job
5.2 years ago cedric • 0
1
vote
0
replies
1.1k
views
Job: Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics gene expression time series plant biology circadian Job
5.4 years ago dezer ▴ 10
2
votes
2
replies
3.9k
views
How adjusted p-values are calculated in limma
limma r transcriptomics FDR statistics
updated 5.4 years ago by 52k • written 5.4 years ago by ▴ 10
2
votes
0
replies
2.6k
views
Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics genomics transcriptomics software Job
5.4 years ago Laurent Gatto 1.6k
1
vote
1
reply
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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0
replies
1.2k
views
Job: Bionformatician Position / Heidelberg
neuroscience data integration transcriptomics Job
5.9 years ago slezak • 0
0
votes
0
replies
988
views
How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r metabolomics KEGG Proteomics Transcriptomics
5.9 years ago Wuschel ▴ 10
1
vote
0
replies
1.8k
views
Job: Full time and permanent research logistician in Bioinformatics
transcriptomics proteomics job bioinformatician Job
6.0 years ago • updated 5.9 years ago Laurent Gatto 1.6k
1
vote
1
reply
1.6k
views
News: Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq deseq2 proteomics transcriptomics workshop News
written 6.0 years ago by 1.6k
3
votes
4
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1.6k
views
Writing a loop to clean up protein names
Proteomics Transcriptomics Loops batch-processing R
updated 6.4 years ago by ▴ 80 • written 6.4 years ago by • 0
48 results • Page 1 of 1
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Comment: DESeq2 It is correct to use interaction term for patient variability? by Bradley • 0
I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
Comment: Differential variance analysis - can i use deseq2 by Michael Love 43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis by Gordon Smyth 52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Comment: WGCNA by pammelala304 • 0
Thank you for your time and effort. I am so grateful! Play game [block blast](https://blockblastpuzzle.io) free.
Comment: Does anyone have the command to download all of the core_nt using blast_db_get() by Matthew Thornton ▴ 380
Ok. So I guess the core_nt is over 300Gb compressed. I can do it, but maybe it is better to just use ncbi-tools over the internet and just…
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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