Showing : RNA-SEQ • reset
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 12 weeks ago by 67k • written 12 weeks ago by ▴ 50
2
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4
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526
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 3 months ago by 42k • written 3 months ago by • 0
1
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2
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495
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
4 months ago Dylan.Sheerin • 0
2
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5
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655
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 10 weeks ago by ★ 4.4k • written 4 months ago by • 0
3
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3
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608
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permutation test in edgeR
rna-seq edgeR
updated 4 months ago by 51k • written 5 months ago by • 0
0
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1
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1.0k
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 8 months ago by ★ 4.4k • written 6.4 years ago by • 0
0
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2
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456
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WGCNA less samples
RNA-Seq WGCNA Worms
9 months ago davca • 0
0
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4
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983
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
11 months ago • updated 10 months ago ar14g12 • 0
0
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2
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3.9k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.1 years ago by ▴ 80
2
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3
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2.6k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 11 months ago by 51k • written 11 months ago by • 0
0
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3
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876
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 12 months ago by ★ 1.9k • written 12 months ago by • 0
3
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4
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1.1k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
13 months ago Eva ▴ 10
0
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3
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834
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 14 months ago by 42k • written 15 months ago by • 0
5
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7
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1.5k
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 15 months ago by 51k • written 15 months ago by ▴ 10
0
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3
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901
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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 16 months ago by 67k • written 16 months ago by • 0
0
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3
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1.0k
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Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 16 months ago by 67k • written 16 months ago by • 0
1
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1
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1.8k
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FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 17 months ago by ★ 4.4k • written 17 months ago by • 0
0
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1
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867
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Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 17 months ago by 67k • written 17 months ago by • 0
2
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2
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920
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Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 17 months ago by ★ 4.4k • written 17 months ago by • 0
0
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1
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790
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
19 months ago Jenny Drnevich ★ 2.0k
0
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1
reply
893
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Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 21 months ago by 42k • written 21 months ago by • 0
5
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9
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2.2k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.1 years ago Yang Shi ▴ 10
2
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2
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1.4k
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.1 years ago Yang Shi ▴ 10
0
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0
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1.0k
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Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.2 years ago eolson • 0
2
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2
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1.1k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.2 years ago by 51k • written 2.2 years ago by • 0
0
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2
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2.8k
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Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 12 months ago by • 0 • written 2.4 years ago by • 0
3
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3
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3.7k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.5 years ago by ▴ 30 • written 5.6 years ago by ▴ 40
5
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5
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1.9k
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First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.5 years ago • updated 2.4 years ago 9906201a ▴ 20
1
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5
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2.3k
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featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.6 years ago Lucy ▴ 60
1
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3
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1.6k
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Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
0
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5
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4.2k
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.6 years ago by ★ 4.4k • written 3.5 years ago by • 0
0
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1
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1.0k
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First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.7 years ago by 51k • written 2.7 years ago by • 0
1
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1
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3.0k
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create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 3.1 years ago by ▴ 10 • written 4.2 years ago by ▴ 10
0
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5
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1.4k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.1 years ago bioinformatic_trainee ▴ 10
0
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0
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1.0k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.1 years ago lianov • 0
0
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1
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1.1k
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.1 years ago slcno • 0
3
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5
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3.0k
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Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.2 years ago by 42k • written 3.2 years ago by ▴ 60
0
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1
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2.0k
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Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.3 years ago by ★ 4.0k • written 3.3 years ago by • 0
2
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3
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1.3k
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Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.3 years ago by 51k • written 3.3 years ago by • 0
5
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2
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23k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.7 years ago by ▴ 30
1
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1
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1.8k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.3 years ago by ★ 1.1k • written 3.3 years ago by ▴ 20
3
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4
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1.2k
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need help regarding differential expression analysis
rna-seq
updated 3.3 years ago by ★ 4.0k • written 3.3 years ago by ▴ 20
0
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0
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1.1k
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Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.3 years ago rbrns • 0
1
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4
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4.1k
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NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.4 years ago by ★ 1.1k • written 7.0 years ago by • 0
3
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4
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1.6k
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Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.4 years ago Antonio M. • 0
1
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2
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1.2k
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multifactorial design matrix
designmatrix RNA-seq limma
updated 3.4 years ago by 51k • written 3.5 years ago by ▴ 20
1
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7
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1.5k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.5 years ago decppced • 0
1
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3
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944
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Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.5 years ago by 42k • written 3.5 years ago by • 0
0
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0
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986
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Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
3.6 years ago wrzl • 0
3
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9
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2.5k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
3.8 years ago • updated 3.7 years ago Pufall, Miles A ▴ 30
50 results • Page 1 of 1
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Comment: SingleR Label.Ont by Stepah • 0
[Aussie Play][1] cares about its Australian players by offering a safe and secure gaming experience where there is never a dull moment. The…
Comment: ensemblVEP deprecation and how to reproduce by Vincent J. Carey, Jr. 6.7k
What aspect of ensemblVEP are you looking for? The vignette https://bioconductor.org/packages/release/bioc/vignettes/VariantAnnotation/in…
Answer: Help with design matrix for RNA-seq data using edgeR by Gordon Smyth 51k
This forum is intended to help with software usage and syntax rather than to answer research questions, and your question is a definitely a…
Answer: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by Michael Love 42k
DESeq2 has a way of fixing the reference pseudo-sample used for normalization. In estimateSizeFactors man page, you will see an argument g…
Comment: [DESeq2] Normalization of External Test Dataset for Machine Learning (ML) Applic by Michael Love 42k
Sorry - I requested this to be posted here, I will answer.
Votes
Answer: Help with design matrix for RNA-seq data using edgeR
Answer: Should tSNE from biol. replicates look alike?
Answer: Should tSNE from biol. replicates look alike?
Comment: fgsea stuck in an infinite loop in the middle of the run
Answer: Empty Results from champ.DMP Despite Expected Output
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