Showing : rna-seq • reset
3
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322
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permutation test in edgeR
rna-seq edgeR
updated 11 days ago by 50k • written 24 days ago by • 0
0
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1
reply
906
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 4 months ago by ★ 4.1k • written 6.0 years ago by • 0
0
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2
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312
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WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
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4
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702
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
7 months ago • updated 6 months ago ar14g12 • 0
0
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2
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3.5k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.8 years ago by ▴ 80
2
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3
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1.6k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
0
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3
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655
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 8 months ago by ★ 1.9k • written 8 months ago by • 0
3
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4
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863
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
0
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3
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682
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 10 months ago by 41k • written 10 months ago by • 0
5
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7
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1.2k
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 11 months ago by 50k • written 11 months ago by ▴ 10
0
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3
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711
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Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization PCR_efficiency bias intrasample_comparison
updated 11 months ago by 65k • written 11 months ago by • 0
0
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3
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848
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Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 11 months ago by 65k • written 11 months ago by • 0
1
vote
1
reply
1.3k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
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1
reply
682
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Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 13 months ago by 65k • written 13 months ago by • 0
2
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2
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721
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Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
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1
reply
659
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
14 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
710
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 17 months ago by 41k • written 17 months ago by • 0
5
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9
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1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
21 months ago Yang Shi ▴ 10
2
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2
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1.2k
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
21 months ago Yang Shi ▴ 10
0
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0
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861
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Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
21 months ago eolson • 0
2
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2
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973
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How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 21 months ago by 50k • written 21 months ago by • 0
0
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2
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2.3k
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Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 8 months ago by • 0 • written 2.1 years ago by • 0
3
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3
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3.3k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.1 years ago by ▴ 30 • written 5.3 years ago by ▴ 30
5
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5
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1.6k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.2 years ago • updated 2.0 years ago 9906201a ▴ 20
1
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5
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2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
1
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3
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1.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
0
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5
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3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.1k • written 3.1 years ago by • 0
0
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1
reply
891
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First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.3 years ago by 50k • written 2.3 years ago by • 0
1
vote
1
reply
2.6k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 2.7 years ago by ▴ 10 • written 3.8 years ago by ▴ 10
0
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5
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1.2k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.7 years ago bioinformatic_trainee ▴ 10
0
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0
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909
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.8 years ago lianov • 0
0
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1
reply
1.0k
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.8 years ago • updated 2.7 years ago slcno • 0
3
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5
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2.6k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 2.9 years ago by 41k • written 2.9 years ago by ▴ 60
0
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1
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1.6k
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Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
2
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3
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1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.9 years ago by 50k • written 2.9 years ago by • 0
5
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2
replies
21k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 2.3 years ago by • 0 • written 5.3 years ago by ▴ 30
1
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1
reply
1.7k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 2.9 years ago by ★ 1.0k • written 2.9 years ago by ▴ 20
3
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4
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1.1k
views
need help regarding differential expression analysis
rna-seq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by ▴ 20
0
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0
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941
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.0 years ago rbrns • 0
1
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4
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3.8k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.0 years ago by ★ 1.0k • written 6.6 years ago by • 0
3
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4
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1.4k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.0 years ago Antonio M. • 0
1
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2
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1.1k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
1
vote
7
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1.4k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.1 years ago decppced • 0
1
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3
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841
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.1 years ago by 41k • written 3.1 years ago by • 0
0
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0
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870
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Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
3.3 years ago wrzl • 0
3
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9
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2.2k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
3.4 years ago Pufall, Miles A ▴ 30
0
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1
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1.0k
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
0
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2
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1.5k
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RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 3.5 years ago by 50k • written 3.5 years ago by ▴ 70
0
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2
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1.2k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 11 months ago by • 0 • written 3.5 years ago by • 0
3
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6
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2.9k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 3.2 years ago by 41k • written 3.5 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
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Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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