Showing : rna-seq • reset
5
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2
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25k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
1
vote
6
replies
842
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 8 days ago by 42k • written 8 days ago by ▴ 10
0
votes
2
replies
259
views
RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
6 weeks ago paul.meraner • 0
0
votes
0
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172
views
WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
8 weeks ago Fernanda • 0
1
vote
3
replies
539
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 5 months ago by 67k • written 5 months ago by ▴ 50
2
votes
4
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642
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 6 months ago by 42k • written 6 months ago by • 0
1
vote
2
replies
586
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
6 months ago Dylan.Sheerin • 0
2
votes
5
replies
877
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 4 months ago by ★ 4.5k • written 6 months ago by • 0
3
votes
3
replies
838
views
permutation test in edgeR
rna-seq edgeR
updated 7 months ago by 51k • written 7 months ago by • 0
0
votes
1
reply
1.1k
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 11 months ago by ★ 4.5k • written 6.6 years ago by • 0
0
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2
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516
views
WGCNA less samples
RNA-Seq WGCNA Worms
12 months ago • updated 11 months ago davca • 0
0
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4
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1.1k
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
13 months ago ar14g12 • 0
0
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2
replies
4.1k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.3 years ago by ▴ 80
2
votes
3
replies
3.2k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 14 months ago by 51k • written 14 months ago by • 0
0
votes
3
replies
954
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 14 months ago by ★ 1.9k • written 14 months ago by • 0
3
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4
replies
1.2k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
15 months ago Eva ▴ 10
0
votes
3
replies
893
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 17 months ago by 42k • written 17 months ago by • 0
5
votes
7
replies
1.6k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 18 months ago by 51k • written 18 months ago by ▴ 10
0
votes
3
replies
975
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 18 months ago by 67k • written 18 months ago by • 0
0
votes
3
replies
1.1k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 18 months ago by 67k • written 18 months ago by • 0
1
vote
1
reply
2.2k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 19 months ago by ★ 4.5k • written 19 months ago by ▴ 10
0
votes
1
reply
965
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 20 months ago by 67k • written 20 months ago by • 0
2
votes
2
replies
1.0k
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 20 months ago by ★ 4.5k • written 20 months ago by • 0
0
votes
1
reply
849
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
21 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
973
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 24 months ago by 42k • written 24 months ago by • 0
5
votes
9
replies
2.3k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.3 years ago Yang Shi ▴ 10
2
votes
2
replies
1.5k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.3 years ago Yang Shi ▴ 10
0
votes
0
replies
1.1k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.3 years ago eolson • 0
2
votes
2
replies
1.2k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.3 years ago by 51k • written 2.3 years ago by • 0
0
votes
2
replies
3.1k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 14 months ago by • 0 • written 2.6 years ago by • 0
3
votes
3
replies
3.9k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.7 years ago by ▴ 30 • written 5.8 years ago by ▴ 40
5
votes
5
replies
2.0k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.7 years ago • updated 2.5 years ago 9906201a ▴ 20
1
vote
5
replies
2.5k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.8 years ago Lucy ▴ 60
1
vote
3
replies
1.7k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.8 years ago by 42k • written 2.8 years ago by • 0
0
votes
5
replies
4.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.8 years ago by ★ 4.5k • written 3.7 years ago by • 0
0
votes
1
reply
1.1k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.8 years ago by 51k • written 2.8 years ago by • 0
1
vote
1
reply
3.2k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 3.3 years ago by ▴ 10 • written 4.4 years ago by ▴ 10
0
votes
5
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1.5k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.3 years ago bioinformatic_trainee ▴ 10
0
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0
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1.1k
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.3 years ago lianov • 0
0
votes
1
reply
1.2k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.3 years ago slcno • 0
3
votes
5
replies
3.2k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.4 years ago by 42k • written 3.4 years ago by ▴ 60
0
votes
1
reply
2.2k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by • 0
2
votes
3
replies
1.4k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.5 years ago by 51k • written 3.5 years ago by • 0
1
vote
1
reply
1.9k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.5 years ago by ★ 1.1k • written 3.5 years ago by ▴ 20
3
votes
4
replies
1.3k
views
need help regarding differential expression analysis
rna-seq
updated 3.5 years ago by ★ 4.0k • written 3.5 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.5 years ago rbrns • 0
1
vote
4
replies
4.3k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.6 years ago by ★ 1.1k • written 7.1 years ago by • 0
3
votes
4
replies
1.6k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.6 years ago Antonio M. • 0
1
vote
2
replies
1.3k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 3.6 years ago by 51k • written 3.6 years ago by ▴ 20
1
vote
7
replies
1.6k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.7 years ago decppced • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: [How to construct a model.matrix ] by kyj2226 • 0
Thanks to you, I learn a lot. Many thanks, Yujin.
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
thank you for your advice, I posted separate post.
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Answer: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Votes
Answer: [How to construct a model.matrix ]
C: DESeq2 baseMean values for each sample
C: DESeq2 baseMean values for each sample
Comment: ColData and ERROR: rows did not converge in beta, labelled in mcols(object)$beta
A: Some questions for remove batch effect by using mnnCorrect
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