Showing : RNA-Seq • reset
2
votes
4
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208
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 2 days ago by 42k • written 5 days ago by • 0
1
vote
2
replies
294
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
13 days ago • updated 12 days ago Dylan.Sheerin • 0
2
votes
3
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266
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 17 days ago by ★ 4.1k • written 19 days ago by • 0
3
votes
3
replies
371
views
permutation test in edgeR
rna-seq edgeR
updated 4 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
1
reply
921
views
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
0
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2
replies
330
views
WGCNA less samples
RNA-Seq WGCNA Worms
6 months ago davca • 0
0
votes
4
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737
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
7 months ago ar14g12 • 0
0
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2
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3.6k
views
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
replies
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
votes
3
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699
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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
replies
899
views
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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714
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 11 months ago by 42k • written 11 months ago by • 0
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 12 months ago by 50k • written 12 months ago by ▴ 10
0
votes
3
replies
745
views
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 66k • written 12 months ago by • 0
0
votes
3
replies
885
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 12 months ago by 66k • written 12 months ago by • 0
1
vote
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
votes
1
reply
715
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 14 months ago by 66k • written 14 months ago by • 0
2
votes
2
replies
748
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
1
reply
689
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
15 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
744
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 18 months ago by 42k • written 18 months ago by • 0
5
votes
9
replies
1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
22 months ago Yang Shi ▴ 10
2
votes
2
replies
1.2k
views
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
0
votes
0
replies
894
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
22 months ago eolson • 0
2
votes
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
votes
2
replies
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
5
votes
5
replies
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 2.1 years ago 9906201a ▴ 20
1
vote
5
replies
2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.3 years ago Lucy ▴ 60
1
vote
3
replies
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
votes
5
replies
3.7k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.4 years ago by ★ 4.1k • written 3.2 years ago by • 0
0
votes
1
reply
915
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.4 years ago by 50k • written 2.4 years ago by • 0
1
vote
1
reply
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
votes
5
replies
1.3k
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
votes
0
replies
931
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.8 years ago lianov • 0
0
votes
1
reply
1.0k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.8 years ago slcno • 0
3
votes
5
replies
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
votes
1
reply
1.6k
views
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
votes
3
replies
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
votes
2
replies
22k
views
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
vote
1
reply
1.7k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.0 years ago by ★ 1.1k • written 3.0 years ago by ▴ 20
3
votes
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
votes
0
replies
969
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.0 years ago rbrns • 0
1
vote
4
replies
3.8k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.1 years ago by ★ 1.1k • written 6.7 years ago by • 0
3
votes
4
replies
1.4k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.1 years ago Antonio M. • 0
1
vote
2
replies
1.1k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 3.1 years ago by 50k • written 3.2 years ago by ▴ 20
1
vote
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
vote
3
replies
859
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
votes
0
replies
889
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
3.3 years ago wrzl • 0
3
votes
9
replies
2.2k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
3.5 years ago • updated 3.4 years ago Pufall, Miles A ▴ 30
0
votes
1
reply
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: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.1k
Hi, What do you get if you run the following `httr::HEAD()` command? I noticed that you have `libcurl` version 8.3.0 from `curl::curl_vers…
Comment: Slightly different count plots from R and spreadsheet by boczniak767 ▴ 720
Thank you @mikelove for your patience and kind advice. So I assume the plots from R are valid. Best wishes.
Answer: Help with infinite recursion - non-zero exit status in installation of GenomeInf by James W. MacDonald 66k
Maybe just try again? ``` > install("GenomeInfoDbData", force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositorie…
Comment: Help with infinite recursion - non-zero exit status in installation of GenomeInf by Brandon • 0
Hello, As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what …
Comment: slingshot: error with plot3d.SlingshotDataSet by Kelly Street • 0
This issue has been addressed [on GitHub][1]. [1]: https://github.com/kstreet13/slingshot/issues/249
Votes
Comment: recount3 problem downloading data from source sra
Answer: Slightly different count plots from R and spreadsheet
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
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