Showing : rna-seq • reset
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34
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
7 hours ago • updated 6 hours ago shaunpeterson • 0
1
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2
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254
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
8 days ago • updated 7 days ago Dylan.Sheerin • 0
2
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3
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253
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 12 days ago by ★ 4.1k • written 14 days ago by • 0
3
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3
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368
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permutation test in edgeR
rna-seq edgeR
updated 26 days ago by 50k • written 5 weeks ago by • 0
0
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1
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917
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 5 months ago by ★ 4.1k • written 6.1 years ago by • 0
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2
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323
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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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733
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
7 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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1.7k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 8 months ago by 50k • written 8 months ago by • 0
0
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3
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688
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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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892
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
0
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3
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710
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 11 months ago by 42k • written 11 months ago by • 0
5
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7
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1.2k
views
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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730
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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 12 months ago by 65k • written 12 months ago by • 0
0
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3
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876
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Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 12 months ago by 65k • written 12 months ago by • 0
1
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1
reply
1.4k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
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1
reply
707
views
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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741
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 13 months ago by ★ 4.1k • written 14 months ago by • 0
0
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1
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685
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
15 months ago Jenny Drnevich ★ 2.0k
0
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1
reply
737
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Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 17 months ago by 42k • written 18 months ago by • 0
5
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9
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1.9k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
22 months ago • updated 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
22 months ago Yang Shi ▴ 10
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0
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887
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Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
22 months ago eolson • 0
2
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2
replies
1.0k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 22 months ago by 50k • written 22 months ago by • 0
0
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2
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2.3k
views
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
votes
3
replies
3.4k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.2 years ago by ▴ 30 • written 5.3 years ago by ▴ 30
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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
2.3 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 2.3 years ago by 42k • written 2.3 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 3.2 years ago by • 0
0
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1
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911
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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
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1
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2.7k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 2.8 years ago by ▴ 10 • written 3.9 years ago by ▴ 10
0
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5
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1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.8 years ago bioinformatic_trainee ▴ 10
0
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0
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925
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
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1.0k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.8 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 42k • 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 3.0 years ago by ★ 3.9k • written 3.0 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 3.0 years ago by 50k • written 3.0 years ago by • 0
5
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2
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22k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 2.3 years ago by • 0 • written 5.4 years ago by ▴ 30
1
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1
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1.7k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.0 years ago by ★ 1.0k • written 3.0 years ago by ▴ 20
3
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4
replies
1.1k
views
need help regarding differential expression analysis
rna-seq
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by ▴ 20
0
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0
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961
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
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NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.1 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
3.1 years ago Antonio M. • 0
1
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2
replies
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
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7
replies
1.4k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.2 years ago decppced • 0
1
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3
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858
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
0
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0
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886
views
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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1.1k
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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