Showing : RNA-seq • reset
1
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 17 days ago by 66k • written 17 days ago by ▴ 50
2
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4
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338
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
1
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2
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360
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
7 weeks ago Dylan.Sheerin • 0
2
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5
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429
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 5 days ago by ★ 4.2k • written 8 weeks ago by • 0
3
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3
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434
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permutation test in edgeR
rna-seq edgeR
updated 9 weeks ago by 51k • written 11 weeks ago by • 0
0
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1
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953
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 6 months ago by ★ 4.2k • written 6.2 years ago by • 0
0
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2
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378
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WGCNA less samples
RNA-Seq WGCNA Worms
7 months ago davca • 0
0
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4
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828
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
8 months ago ar14g12 • 0
0
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2
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3.7k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.9 years ago by ▴ 80
2
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3
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2.0k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 9 months ago by 51k • written 9 months ago by • 0
0
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3
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755
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
3
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4
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956
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
10 months ago Eva ▴ 10
0
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3
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763
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 12 months ago by 42k • written 12 months ago by • 0
5
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7
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1.3k
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 13 months ago by 51k • written 13 months ago by ▴ 10
0
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3
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796
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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 13 months ago by 66k • written 13 months ago by • 0
0
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3
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935
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 13 months ago by 66k • written 13 months ago by • 0
1
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1
reply
1.5k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
0
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1
reply
758
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Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 15 months ago by 66k • written 15 months ago by • 0
2
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2
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794
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Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 15 months ago by ★ 4.2k • written 15 months ago by • 0
0
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1
reply
726
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
16 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
793
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 19 months ago by 42k • written 19 months ago by • 0
5
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9
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2.0k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
23 months ago Yang Shi ▴ 10
2
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2
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1.3k
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
23 months ago Yang Shi ▴ 10
0
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0
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930
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Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
23 months ago eolson • 0
2
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2
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1.0k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 23 months ago by 51k • written 23 months ago by • 0
0
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2
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2.5k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 10 months ago by • 0 • written 2.2 years ago by • 0
3
votes
3
replies
3.5k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.3 years ago by ▴ 30 • written 5.4 years ago by ▴ 40
5
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5
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1.7k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.3 years ago • updated 2.2 years ago 9906201a ▴ 20
1
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5
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2.1k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.4 years ago Lucy ▴ 60
1
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3
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1.5k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.4 years ago by 42k • written 2.4 years ago by • 0
0
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5
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3.8k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.5 years ago by ★ 4.2k • written 3.3 years ago by • 0
0
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1
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943
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First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.5 years ago by 51k • written 2.5 years ago by • 0
1
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1
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2.8k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 2.9 years ago by ▴ 10 • written 4.0 years ago by ▴ 10
0
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5
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1.3k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.9 years ago bioinformatic_trainee ▴ 10
0
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0
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956
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.9 years ago lianov • 0
0
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1
reply
1.1k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.9 years ago slcno • 0
3
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5
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2.8k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.0 years ago by 42k • written 3.0 years ago by ▴ 60
0
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1
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1.7k
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Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.1 years ago by ★ 3.9k • written 3.1 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 3.1 years ago by 51k • written 3.1 years ago by • 0
5
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2
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22k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 2.4 years ago by • 0 • written 5.5 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 3.1 years ago by ★ 1.1k • written 3.1 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 3.1 years ago by ★ 3.9k • written 3.1 years ago by ▴ 20
0
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0
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1000
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Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.1 years ago rbrns • 0
1
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4
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3.9k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.2 years ago by ★ 1.1k • written 6.8 years ago by • 0
3
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4
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1.5k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.2 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 3.2 years ago by 51k • written 3.3 years ago by ▴ 20
1
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7
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1.4k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.3 years ago decppced • 0
1
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3
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886
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.3 years ago by 42k • written 3.3 years ago by • 0
0
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0
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918
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
3.4 years ago wrzl • 0
3
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9
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2.3k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
3.6 years ago • updated 3.5 years ago Pufall, Miles A ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Answer: Ranking the GSEA Results by Michael Love 42k
Some posts on this topic: https://www.google.com/search?q=site%3Asupport.bioconductor.org+GSEA+ranking+DESeq2
Answer: Advice on appropriateness of an offset in glmGamPoi/edgeR by Gordon Smyth 51k
edgeR allows observation specific offsets (as already pointed out), although I am not confident that would be a reliable solution to your p…
Comment: Research Project - Expanding search funtionality on the GEO database by gallantk5 • 0
Thank you I will take a look at those !
Comment: Research Project - Expanding search funtionality on the GEO database by gallantk5 • 0
I will send you an email and talk to my advisor about setting up a meeting. Thank you !
Comment: Research Project - Expanding search funtionality on the GEO database by Sean Davis 21k
You can use the Bioconductor Annotation packages for the Affymetrix chips of interest. - https://bioconductor.org/packages/release/BiocVie…
Votes
Answer: DESeq2 time course using fitted splines
Answer: DESeq2 time course using fitted splines
Comment: Difference between enrichGO results and Enrichr website results
Answer: Struggling to convert a large list of non-model genes into human orthologs, any
A: makeContrasts from limma overides "i" as a varible
Awards • All
Popular Question to Gordon Smyth 51k
Popular Question to Sean Davis 21k
Popular Question to Guido Hooiveld ★ 4.0k
Scholar to Martin Morgan 25k
Popular Question to Wolfgang Huber ★ 13k
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