Showing : RNASeq • reset
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Genes with highest differential expression have very low read counts for most genes
RNASeq depmap DESeq2
updated 4 days ago by 40k • written 13 days ago by • 0
3
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11
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491
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Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
13 days ago • updated 3 days ago Anna ▴ 20
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9
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3.9k
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how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 5.3 years ago by • 0
0
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1
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148
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CI for logCPM (fitted values)
RNAseq edgeR
updated 19 days ago by 47k • written 19 days ago by ▴ 10
3
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4
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229
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Anova table edgeR limma
limma RNASeq edgeR
27 days ago • updated 26 days ago KATHERINE CHUERE NUNES • 0
1
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2
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141
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Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 29 days ago by 47k • written 29 days ago by • 0
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3
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266
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Account for heteroscedasticity when fitting gene expression data
RNAseq
updated 27 days ago by 40k • written 4 weeks ago by • 0
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2
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173
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 4 weeks ago by • 0
1
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3
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223
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Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 4 weeks ago by 47k • written 5 weeks ago by • 0
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2
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179
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model matrix not full rank
DESeq2 RNASeq
updated 4 weeks ago by • 0 • written 5 weeks ago by • 0
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1
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155
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What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2 RNASeq
updated 5 weeks ago by 40k • written 7 weeks ago by • 0
2
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3
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186
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RNA seq with edgeR with several factors
RNAseq factors
6 weeks ago • updated 5 weeks ago Nathalie ▴ 20
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3
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222
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edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 5 weeks ago by 47k • written 6 weeks ago by • 0
7
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8
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8.5k
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GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 6 weeks ago by ★ 2.9k • written 6.9 years ago by ▴ 10
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4
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219
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Combine RNA-seq
BatchEffect R rnaseq
updated 6 weeks ago by ★ 1.2k • written 6 weeks ago by • 0
1
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1
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198
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Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 6 weeks ago by 47k • written 6 weeks ago by • 0
3
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12
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457
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Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 7 weeks ago by 40k • written 7 weeks ago by ▴ 10
0
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1
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149
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Sample expression calculation in rna seq
Rnaseq
updated 7 weeks ago by ★ 2.9k • written 7 weeks ago by • 0
1
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1
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134
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Can I run deseq2 on two separate experiments at once?
rnaseq deseq2
updated 8 weeks ago by ★ 2.9k • written 8 weeks ago by • 0
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142
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WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
9 weeks ago Levi • 0
4
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8
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2.0k
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Interpreting ellipses in PCAtools for bulk RNAseq
ellipse RNAseq PCAtools
updated 9 weeks ago by • 0 • written 2.0 years ago by • 0
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2
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188
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RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 9 weeks ago by • 0
2
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4
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270
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limma with or without intercept gives different results
limma rnaseq
10 weeks ago Sydney • 0
1
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2
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275
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RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
10 weeks ago garbuzov • 0
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2
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146
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Compare and filter three BAM files
RNAseq 10X
11 weeks ago • updated 10 weeks ago wt215 • 0
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5
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306
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hill-shaped p-value distributions using EdgeR
edgeR p-valuedistribution RNAseq hill-shaped
updated 11 weeks ago by 47k • written 12 weeks ago by • 0
5
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6
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370
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different number of DEG because of outliers
DESeq2 RNASeq
updated 11 weeks ago by ▴ 40 • written 12 weeks ago by • 0
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2
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183
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GO analysis in R vs website
GO RNASeq
12 weeks ago Nitro • 0
1
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4
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262
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Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
12 weeks ago DH • 0
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258
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Job: Seeking collaborator/contractor (paid) for Bioconductor package development
RNASeq JobPosting
12 weeks ago Jamie Walters ▴ 10
3
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2
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175
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
3 months ago chf • 0
0
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1
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169
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 3 months ago by ★ 2.9k • written 3 months ago by • 0
1
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1
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159
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Subsetting DESeq when different cell types
DESeq2 RNASeq
updated 3 months ago by ★ 2.9k • written 3 months ago by ▴ 20
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7
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505
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Weird dispersion and volcano plots in DEA with paired samples
DESeq2 RNASeq
updated 11 weeks ago by 40k • written 3 months ago by • 0
0
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2
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288
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PCA subset of genes vs DE
DESeq2 RNASeq
3 months ago andrebolerbarros ▴ 20
2
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5
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343
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 3 months ago by • 0
0
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3
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277
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Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 3 months ago by 47k • written 3 months ago by • 0
0
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2
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225
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combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 3 months ago by ★ 2.9k • written 3 months ago by • 0
0
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1
reply
202
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
updated 3 months ago by ★ 2.9k • written 3 months ago by • 0
6
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11
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579
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Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
3 months ago mohammedtoufiq91 ▴ 10
2
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1
reply
201
views
EdgeR model matrix
edgeR RNASeq
updated 4 months ago by 63k • written 4 months ago by • 0
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2
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325
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Which genes are outliers in DESeq2?
DESeq2 RNAseq outlier
updated 4 months ago by ★ 2.9k • written 4 months ago by • 0
2
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10
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585
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edgeR: Usage of estimated dispersion from replicates for pools of the same experiment
edgeR RNAseq
updated 4 months ago by 47k • written 4 months ago by • 0
2
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2
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269
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Calculate transcriptional heterogeneity for a condition using DESeq2
RNASeq
5 months ago • updated 4 months ago SciencyUsagi ▴ 10
0
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1
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302
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Variance stabilization transformation (VST), blind=TRUE
DESeq2 Transcriptomics RNASeq
updated 4 months ago by 40k • written 4 months ago by • 0
3
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3
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724
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Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 4 months ago by 47k • written 4 months ago by • 0
0
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3
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370
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Gene TPM validity with STAR only quantification
RNASeq
written 5 months ago by ▴ 10
2
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5
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478
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Create the design matrix
DEGseq edgeR RNASeq
5 months ago Mohammad • 0
2
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5
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804
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How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
updated 4 months ago by 47k • written 5 months ago by ▴ 10
0
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3
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361
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DESeq2 Statistic - Padj NA
DESeq2 RNAseq123 rnaseq deseq2 metatranscriptomic
updated 5 months ago by 40k • written 5 months ago by • 0
50 results • Page 1 of 1
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Answer: multiple filters in biomaRt by RuBBiT0 ▴ 10
First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use. Second, could you pro…
Comment: Diffbind "No genome detected" by kyliecode • 0
Hi Dr. Stark, Thanks very much for your reply! The bam files were output from nf-core/chipseq pipeline and for some reason, they do not ha…
Answer: Discrepancy between DESeq2 files produced in Galaxy and R(RStudio) by Michael Love 40k
I guess that Galaxy may be using some kind of LFC shrinkage, but without seeing their code I wouldn't know for sure. Shrinkage generally…
Comment: TCGAbiolinks cannot find bcr_patient_barcode by Habil Zare ▴ 170
I checked your example with the devel version 2.29.6 on Bioc and it worked fine. Thanks for the fix!
Answer: error in ChAMP loading file by jenniferbrowngates • 0
I got a lot of information from this website about different topics which is beneficial for me too so I thank this site and also suggest a …
Votes
Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Comment: Error: biomaRt has encountered an unexpected server error.
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
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