Showing : RNA-SEQ • reset
3
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permutation test in edgeR
rna-seq edgeR
updated 2 days ago by 50k • written 9 days ago by • 0
0
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1
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892
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 4 months ago by ★ 4.0k • written 6.0 years ago by • 0
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2
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294
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WGCNA less samples
RNA-Seq WGCNA Worms
4 months ago davca • 0
0
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4
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659
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
6 months ago ar14g12 • 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 3.7 years ago by ▴ 80
2
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3
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1.5k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
0
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3
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630
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 7 months ago by ★ 1.9k • written 7 months ago by • 0
3
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4
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836
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
0
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3
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656
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 10 months ago by 41k • written 10 months ago by • 0
5
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7
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 10 months ago by 50k • written 10 months ago by ▴ 10
0
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3
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687
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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 11 months ago by 65k • written 11 months ago by • 0
0
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3
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826
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Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 11 months ago by 65k • written 11 months ago by • 0
1
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1
reply
1.2k
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FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 12 months ago by ★ 4.0k • written 12 months ago by • 0
0
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1
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660
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Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 12 months ago by 65k • written 12 months ago by • 0
2
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2
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699
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Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 12 months ago by ★ 4.0k • written 13 months ago by • 0
0
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1
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626
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
14 months ago Jenny Drnevich ★ 2.0k
0
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1
reply
685
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Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 16 months ago by 41k • written 17 months ago by • 0
5
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9
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1.8k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
21 months ago • updated 20 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
21 months ago Yang Shi ▴ 10
0
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0
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841
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Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
21 months ago eolson • 0
2
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2
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950
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How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 21 months ago by 50k • written 21 months ago by • 0
0
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2
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Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 7 months ago by • 0 • written 2.0 years ago by • 0
3
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3
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3.3k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.1 years ago by ▴ 30 • written 5.2 years ago by ▴ 30
5
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5
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1.6k
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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
2.1 years ago • updated 23 months ago 9906201a ▴ 20
1
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5
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1.9k
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featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
1
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3
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1.4k
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Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
0
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5
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3.5k
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
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1
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874
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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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2.6k
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create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 2.7 years ago by ▴ 10 • written 3.8 years ago by ▴ 10
0
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5
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1.2k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.7 years ago bioinformatic_trainee ▴ 10
0
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887
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.7 years ago lianov • 0
0
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1
reply
986
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.7 years ago slcno • 0
3
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5
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2.5k
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Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 2.8 years ago by 41k • written 2.8 years ago by ▴ 60
0
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1
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1.5k
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Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
2
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3
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1.2k
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Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.9 years ago by 50k • written 2.9 years ago by • 0
5
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2
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21k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 2.2 years ago by • 0 • written 5.3 years ago by ▴ 30
1
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1
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1.7k
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Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 2.9 years ago by ★ 1.0k • written 2.9 years ago by ▴ 20
3
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4
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1.1k
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need help regarding differential expression analysis
rna-seq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by ▴ 20
0
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0
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918
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Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
2.9 years ago rbrns • 0
1
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4
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3.7k
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NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.0 years ago by ★ 1.0k • written 6.6 years ago by • 0
3
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4
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1.4k
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Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.0 years ago Antonio M. • 0
1
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2
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1.1k
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multifactorial design matrix
designmatrix RNA-seq limma
updated 3.0 years ago by 50k • written 3.1 years ago by ▴ 20
1
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7
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1.4k
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how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.1 years ago decppced • 0
1
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3
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832
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Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.1 years ago by 41k • written 3.1 years ago by • 0
0
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0
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862
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Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
3.2 years ago wrzl • 0
3
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9
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summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
3.4 years ago • updated 3.3 years ago Pufall, Miles A ▴ 30
0
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1
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1.0k
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Limma/Voom Normalized Counts
limma RNA-seq
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
0
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2
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1.5k
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RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 3.4 years ago by 50k • written 3.4 years ago by ▴ 70
0
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2
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1.2k
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Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 11 months ago by • 0 • written 3.5 years ago by • 0
3
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6
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2.9k
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DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 3.2 years ago by 41k • written 3.5 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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