Showing : RNA-Seq • reset
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 10 weeks ago by 52k • written 10 weeks ago by ▴ 80
5
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3
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28k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.3 years ago by ▴ 30
1
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6
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1.3k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 5 months ago by 43k • written 5 months ago by ▴ 10
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2
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486
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
6 months ago paul.meraner • 0
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384
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
7 months ago Fernanda • 0
1
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3
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773
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 10 months ago by 68k • written 10 months ago by ▴ 50
2
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4
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856
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 11 months ago by 43k • written 11 months ago by • 0
1
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2
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829
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
11 months ago Dylan.Sheerin • 0
2
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6
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1.7k
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 7 weeks ago by • 0 • written 11 months ago by • 0
3
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3
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1.4k
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permutation test in edgeR
rna-seq edgeR
updated 12 months ago by 52k • written 12 months ago by • 0
0
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1
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1.2k
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 16 months ago by ★ 4.8k • written 7.0 years ago by • 0
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2
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624
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WGCNA less samples
RNA-Seq WGCNA Worms
17 months ago davca • 0
0
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4
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1.3k
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
19 months ago • updated 18 months ago ar14g12 • 0
0
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2
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4.5k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.8 years ago by ▴ 80
2
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3
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4.3k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 19 months ago by 52k • written 19 months ago by • 0
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3
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 20 months ago by ★ 1.9k • written 20 months ago by • 0
3
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4
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1.6k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
20 months ago Eva ▴ 10
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3
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1.0k
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 22 months ago by 43k • written 22 months ago by • 0
5
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7
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1.8k
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 23 months ago by 52k • written 23 months ago by ▴ 10
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3
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1.1k
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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 23 months ago by 68k • written 23 months ago by • 0
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3
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1.3k
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Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 23 months ago by 68k • written 23 months ago by • 0
1
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1
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2.9k
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FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 2.0 years ago by ★ 4.8k • written 2.0 years ago by ▴ 10
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1
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1.3k
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Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
2
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2
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1.2k
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Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 2.1 years ago by ★ 4.8k • written 2.1 years ago by • 0
0
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1
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951
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
2.2 years ago Jenny Drnevich ★ 2.0k
0
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1
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1.1k
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Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
5
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9
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2.6k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.8 years ago • updated 2.7 years ago Yang Shi ▴ 10
2
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2
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1.7k
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.8 years ago Yang Shi ▴ 10
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0
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1.2k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.8 years ago eolson • 0
2
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2
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1.4k
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How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
0
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2
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3.7k
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Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 20 months ago by • 0 • written 3.0 years ago by • 0
3
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3
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4.3k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.1 years ago by ▴ 30 • written 6.3 years ago by ▴ 40
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5
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2.5k
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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
3.2 years ago • updated 3.0 years ago 9906201a ▴ 20
1
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5
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3.0k
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featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.2 years ago Lucy ▴ 60
1
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3
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1.9k
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Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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5
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5.4k
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.3 years ago by ★ 4.8k • written 4.1 years ago by • 0
0
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1
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1.2k
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First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 3.3 years ago by 52k • written 3.3 years ago by • 0
1
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1
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3.6k
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create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 3.7 years ago by ▴ 10 • written 4.8 years ago by ▴ 10
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5
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1.7k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.7 years ago bioinformatic_trainee ▴ 10
0
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1.2k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.7 years ago lianov • 0
0
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1
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1.3k
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.8 years ago • updated 3.7 years ago slcno • 0
3
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5
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3.8k
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Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.9 years ago by 43k • written 3.9 years ago by ▴ 60
0
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1
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2.7k
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Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by • 0
2
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3
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1.6k
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Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.9 years ago by 52k • written 3.9 years ago by • 0
1
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1
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2.1k
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Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.9 years ago by ★ 1.1k • written 3.9 years ago by ▴ 20
3
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4
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1.5k
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need help regarding differential expression analysis
rna-seq
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by ▴ 20
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0
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1.2k
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Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.9 years ago rbrns • 0
1
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4
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4.7k
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NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4.0 years ago by ★ 1.1k • written 7.6 years ago by • 0
3
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4
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1.8k
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Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
4.0 years ago Antonio M. • 0
1
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2
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1.4k
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multifactorial design matrix
designmatrix RNA-seq limma
updated 4.1 years ago by 52k • written 4.1 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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