Showing : Rnaseq • reset
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hill-shaped p-value distributions using EdgeR
edgeR p-valuedistribution RNAseq hill-shaped
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
5
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7
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1.8k
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different number of DEG because of outliers
DESeq2 RNASeq
updated 2.1 years ago by 53k • written 3.0 years ago by • 0
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2
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1.8k
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GO analysis in R vs website
GO RNASeq
3.0 years ago Nitro • 0
1
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4
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1.6k
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
3.0 years ago DH • 0
1
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0
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1.3k
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Job: Seeking collaborator/contractor (paid) for Bioconductor package development
RNASeq JobPosting
3.0 years ago Jamie Walters ▴ 10
3
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2
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
3.0 years ago chf • 0
1
vote
3
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2.1k
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 22 months ago by ★ 1.2k • written 3.0 years ago by ▴ 10
1
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1
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1.0k
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Subsetting DESeq when different cell types
DESeq2 RNASeq
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by ▴ 20
0
votes
7
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2.5k
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Weird dispersion and volcano plots in DEA with paired samples
DESeq2 RNASeq
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
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3
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1.5k
views
PCA subset of genes vs DE
DESeq2 RNASeq
written 3.0 years ago by ▴ 20
2
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5
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2.9k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 3.0 years ago by • 0
0
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3
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1.6k
views
Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
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2
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1.9k
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combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by • 0
0
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2
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5.1k
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 3.0 years ago by • 0
6
votes
11
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2.6k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
3.0 years ago mohammedtoufiq91 ▴ 10
2
votes
1
reply
818
views
EdgeR model matrix
edgeR RNASeq
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
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2
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2.2k
views
Which genes are outliers in DESeq2?
DESeq2 RNAseq outlier
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
2
votes
10
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2.1k
views
edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
2
votes
2
replies
833
views
Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
3.1 years ago SciencyUsagi ▴ 10
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1
reply
3.3k
views
Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 3.1 years ago by 43k • written 3.1 years ago by • 0
3
votes
3
replies
7.4k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
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3
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1.5k
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Gene TPM validity with STAR only quantification
RNASeq
written 3.2 years ago by ▴ 10
2
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5
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1.9k
views
Create the design matrix
DEGseq edgeR RNASeq
3.2 years ago Mohammad • 0
4
votes
5
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7.1k
views
How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
updated 3.1 years ago by 53k • written 3.2 years ago by ▴ 10
0
votes
3
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1.8k
views
DESeq2 Statistic - Padj NA
DESeq2 RNAseq123 rnaseq deseq2 metatranscriptomic
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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0
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557
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A problem with Experimental Design for Limma
limma RNASeq
3.2 years ago ToReality • 0
0
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3
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2.7k
views
Unusual MA and volcano plots?
DESeq2 RNASeq
written 3.2 years ago by ▴ 10
0
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1
reply
1.2k
views
Job: 'Omics data analyst for HPCBio, University of Illinois
SingleCell rnaseq methylationArrayAnalysis Spatial
written 3.2 years ago by ★ 2.0k
1
vote
2
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1.3k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
3.2 years ago mohammedtoufiq91 ▴ 10
0
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0
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580
views
RNA seq analysis
RNASeq
3.2 years ago lesseyl • 0
2
votes
3
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2.5k
views
Error while reading rsem files in tximport
DESeq2 tximport rsem RNASeq tximportData
3.2 years ago mohammedtoufiq91 ▴ 10
0
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1
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1.3k
views
TCGA RNAseq Normalization
normalization RNASEQ Normalization TCGAutils TCGA
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
2
votes
4
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6.3k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
3.3 years ago mohammedtoufiq91 ▴ 10
0
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1
reply
1.3k
views
Interpretation of coefficient when using "~ grp + grp:ind.n + grp:cnd"
DESeq2 interaction coefficient LinearModel RNASeq
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
1
vote
1
reply
4.2k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
0
votes
4
replies
1.6k
views
Higher Dimensional RNASeq Clustering Significance
DESeq2 RNASeq PrincipalComponent pcaExplorer
written 3.3 years ago by • 0
1
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2
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1.6k
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.3 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.6k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
0
votes
0
replies
1.2k
views
Job: EPA Postdoctoral Fellowship in Bioinformatics and Computational Toxicology
MethylSeq Transcriptomics Pathways Epigenetics RNASeq
3.3 years ago whduke • 0
0
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3
replies
2.7k
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 19 months ago by • 0 • written 3.3 years ago by • 0
0
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3
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3.5k
views
Gene ontology enrichment analysis
rnaseq rnaseqGene geneontology
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
0
votes
1
reply
839
views
Analysing only significant genes from differential expression analysis in a replication cohort
RNASeq
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
2
votes
3
replies
2.6k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
0
votes
2
replies
1.4k
views
RNA-Seq Reads Count
DESeq2 htseq DEGseq RNASeq read
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
3
votes
7
replies
3.0k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
1
vote
2
replies
1.6k
views
Design formula with batch effects DESeq2 "Not full rank matrix" error.
DESeq2 BatchEffect RNASeq
updated 3.4 years ago by ★ 1.4k • written 3.4 years ago by • 0
0
votes
0
replies
1.1k
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.4 years ago rridley3 • 0
3
votes
16
replies
3.7k
views
Atena package - error (new user)
RNAseq R Atena
3.4 years ago • updated 3.1 years ago lalanis1 • 0
2
votes
5
replies
4.8k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 3.4 years ago by 43k • written 4.7 years ago by • 0
0
votes
1
reply
2.1k
views
Does DeSeq2 make comparisons between all samples vs. all controls, or between matched samples and controls in different groups?
DESeq2 RNAseq bulk DifferentialExpression
updated 3.4 years ago by 68k • written 3.4 years ago by • 0
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Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
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Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
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Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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