Showing : Transcriptomics • reset
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Filtering Steps for proActiv Analysis
Transcriptomics proActiv
7 weeks ago LuciaNhu • 0
1
vote
6
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732
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New to Deseq2 - DEG questions / MA plot
genomes DESeq2 Transcriptomics
updated 9 weeks ago by ★ 4.6k • written 12 weeks ago by • 0
0
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0
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240
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proActiv-promoter analysis
proActiv Transcriptomics
4 months ago wang.xiangyu • 0
0
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0
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368
views
Job: Postdoctoral fellowships in Spatial Omics and Single Cell Genomics at the University of Padova (IT)
SingleCell Transcriptomics SpatialDatasets SpatialData
6 months ago Silvio • 0
3
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2
replies
491
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
9 months ago Anita ▴ 10
4
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5
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2.5k
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DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
0
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4
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1.0k
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
19 months ago sreeshmaraj72 • 0
0
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1
reply
516
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Time change in expression vs time change in phenotype
Transcriptomics ExpressionData DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
4
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5
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2.7k
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EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
Transcriptomics EnhancedVolcano
updated 20 months ago by ★ 4.0k • written 20 months ago by ▴ 20
4
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8
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1.8k
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DESEQ2 - What is the recommended workflow in terms of pre-filtering and counts normalization?
DESeq2 Transcriptomics
updated 20 months ago by ★ 13k • written 20 months ago by ▴ 20
0
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3
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1.0k
views
Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 22 months ago by 52k • written 22 months ago by • 0
0
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1
reply
965
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2 Transcriptomics tximport deseq txi
updated 23 months ago by ★ 1.5k • written 23 months ago by ▴ 10
0
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1
reply
2.0k
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Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 23 months ago by 43k • written 23 months ago by • 0
0
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0
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741
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Analysis of TIF-seq data to generate transcription start sites (TSS) and poly(A) site (PAS) clusters
Transcriptomics SequencingData
2.1 years ago Rom • 0
0
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0
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835
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Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
2.1 years ago whduke • 0
0
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2
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876
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Questions about `collapseReplicates` function in DESeq2
DESeq2 Transcriptomics
2.2 years ago Yijing • 0
0
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0
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691
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WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
2.3 years ago Julieta • 0
2
votes
1
reply
2.6k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by ▴ 10
0
votes
3
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1.3k
views
DESeq2 - transcript length correction necessary when quantifying reads from ends of transcripts?
Transcriptomics DESeq2
2.4 years ago marius.wenzel • 0
4
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6
replies
1.8k
views
How to best visualize multi-level transcriptomics experiment data?
ggplot2 Transcriptomics Visualization R limma
2.6 years ago mohammedtoufiq91 ▴ 10
1
vote
3
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1.4k
views
Identifying DEG between development stages
plant Transcriptomics DESeq2 r
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
2
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5
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1.6k
views
DESeq2 with baseline correction for gene expression differences
DESeq2 edgeR Transcriptomics
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
2
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2
replies
1.1k
views
Deseq2 Resul variation by LFC variation
rnaseqGene DESeq2 Transcriptomics
3.2 years ago • updated 19 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
3.3 years ago Barista • 0
0
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0
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1.1k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.4 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
3.4 years ago marie • 0
0
votes
2
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1.4k
views
Downloading org.Mm.eg.db after R reinstall
org.Mmu.eg.db Transcriptomics
3.7 years ago Kate • 0
0
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0
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1.1k
views
Consensus wgcna soft threshold for each data
Transcriptomics WGCNA wgcna
3.8 years ago 2323982403 ▴ 60
0
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1
reply
931
views
Metatranscriptomics DESeq2 multifactorial sampling
Transcriptomics DESeq2
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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0
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1.1k
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Job: Bioinformatician at MiroBio, Oxford, UK
Transcriptomics Bioconductor Statistics Job Biocon
3.8 years ago m.jackson • 0
5
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5
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3.2k
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analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 3.8 years ago by 67k • written 3.8 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
4.0 years ago Steve Lianoglou ★ 13k
1
vote
1
reply
1.1k
views
NanoStringDiff Not Recognized as Numeric
Bioconductor Transcriptomics NanoStringDiff
updated 4.1 years ago by 1.6k • written 4.1 years ago by ▴ 10
0
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0
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856
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Problems with cummeRbund
plot transcriptomics differential expression cummeRbund
4.7 years ago raquelponti • 0
1
vote
0
replies
1.2k
views
News: News: Bioinformatics Summer School - July 2020 - UCLouvain (Belgium)
rnaseq course proteomics transcriptomics scrnaseq News
4.9 years ago Laurent Gatto 1.6k
0
votes
4
replies
1.3k
views
GOexpress - Error when plotting expression data
RNA-seq transcriptomics gene ontology gene expression GOexpress
updated 4.9 years ago by ▴ 350 • written 4.9 years ago by • 0
0
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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
5.0 years ago Joseph Barry ▴ 10
0
votes
0
replies
902
views
Job: Bionformatician in personalized oncotherapy (BEL)
job bioinformatician immunotherapy genomics transcriptomics Job
5.1 years ago cedric • 0
1
vote
0
replies
1.0k
views
Job: Bioinformatics PhD: The circadian clock in the ageing plant, University of York, UK
transcriptomics gene expression time series plant biology circadian Job
5.2 years ago dezer ▴ 10
2
votes
2
replies
3.7k
views
How adjusted p-values are calculated in limma
limma r transcriptomics FDR statistics
updated 5.2 years ago by 52k • written 5.2 years ago by ▴ 10
2
votes
0
replies
2.5k
views
Job: Bioconductor infrastructure for the integration of genomics, transcriptomics and proteomics data
proteomics genomics transcriptomics software Job
5.2 years ago Laurent Gatto 1.6k
1
vote
1
reply
1.1k
views
cpm filtering parameter
cpm filtering transcriptomics rnaseq edgeR metatranscriptomics
updated 5.3 years ago by 52k • written 5.3 years ago by ▴ 10
0
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0
replies
1.1k
views
Job: Bionformatician Position / Heidelberg
neuroscience data integration transcriptomics Job
5.7 years ago slezak • 0
0
votes
0
replies
939
views
How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r metabolomics KEGG Proteomics Transcriptomics
5.7 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
5.8 years ago • updated 5.7 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 5.8 years ago by 1.6k
3
votes
4
replies
1.5k
views
Writing a loop to clean up protein names
Proteomics Transcriptomics Loops batch-processing R
updated 6.2 years ago by ▴ 80 • written 6.2 years ago by • 0
47 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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