Showing : rna-seq • reset
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 3 months ago by 52k • written 3 months ago by ▴ 80
5
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3
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28k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.4 years ago by ▴ 30
1
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6
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1.3k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 6 months ago by 43k • written 6 months ago by ▴ 10
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2
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508
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
7 months ago paul.meraner • 0
0
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0
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443
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
8 months ago Fernanda • 0
1
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3
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797
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 11 months ago by 68k • written 11 months ago by ▴ 50
2
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4
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893
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 12 months ago by 43k • written 12 months ago by • 0
1
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2
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858
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
12 months ago Dylan.Sheerin • 0
2
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6
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1.9k
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 11 weeks ago by • 0 • written 12 months ago by • 0
3
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3
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1.5k
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permutation test in edgeR
rna-seq edgeR
updated 13 months ago by 52k • written 13 months ago by • 0
0
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1
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1.3k
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 17 months ago by ★ 4.8k • written 7.1 years ago by • 0
0
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2
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649
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WGCNA less samples
RNA-Seq WGCNA Worms
18 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 ar14g12 • 0
0
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2
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4.6k
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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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4.5k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 20 months ago by 52k • written 20 months ago by • 0
0
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3
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1.1k
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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
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
21 months ago Eva ▴ 10
0
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3
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1.1k
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 23 months ago by 43k • written 23 months ago by • 0
5
votes
7
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1.9k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 24 months ago by 52k • written 24 months ago by ▴ 10
0
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3
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1.1k
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 2.0 years ago by 68k • written 2.0 years ago by • 0
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 2.0 years ago by 68k • written 2.0 years ago by • 0
1
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1
reply
3.0k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 2.1 years ago by ★ 4.8k • written 2.1 years ago by ▴ 10
0
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1
reply
1.3k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
2
votes
2
replies
1.2k
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 2.2 years ago by ★ 4.8k • written 2.2 years ago by • 0
0
votes
1
reply
969
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
2.3 years ago Jenny Drnevich ★ 2.0k
0
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1
reply
1.1k
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 2.5 years ago by 43k • written 2.5 years ago by • 0
5
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9
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2.7k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.8 years ago Yang Shi ▴ 10
2
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2
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1.8k
views
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
0
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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
2.9 years ago eolson • 0
2
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2
replies
1.5k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.9 years ago by 52k • written 2.9 years ago by • 0
0
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2
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3.9k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 20 months ago by • 0 • written 3.1 years ago by • 0
3
votes
3
replies
4.4k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.2 years ago by ▴ 30 • written 6.3 years ago by ▴ 40
5
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5
replies
2.8k
views
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 3.1 years ago 9906201a ▴ 20
1
vote
5
replies
3.1k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.3 years ago Lucy ▴ 60
1
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3
replies
1.9k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
5
replies
5.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.4 years ago by ★ 4.8k • written 4.2 years ago by • 0
0
votes
1
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1.2k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 3.4 years ago by 52k • written 3.4 years ago by • 0
1
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1
reply
3.7k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 3.8 years ago by ▴ 10 • written 4.9 years ago by ▴ 10
0
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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
3.8 years ago bioinformatic_trainee ▴ 10
0
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0
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1.2k
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.8 years ago lianov • 0
0
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1
reply
1.3k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.8 years ago slcno • 0
3
votes
5
replies
4.0k
views
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
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by • 0
2
votes
3
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1.6k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 4.0 years ago by 52k • written 4.0 years ago by • 0
1
vote
1
reply
2.2k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 4.0 years ago by ★ 1.1k • written 4.0 years ago by ▴ 20
3
votes
4
replies
1.5k
views
need help regarding differential expression analysis
rna-seq
updated 4.0 years ago by ★ 4.0k • written 4.0 years ago by ▴ 20
0
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0
replies
1.2k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
4.0 years ago rbrns • 0
1
vote
4
replies
4.8k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4.1 years ago by ★ 1.1k • written 7.7 years ago by • 0
3
votes
4
replies
1.8k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
4.1 years ago Antonio M. • 0
1
vote
2
replies
1.4k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 4.1 years ago by 52k • written 4.2 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: parameters of filterByExpr by caroline.zanchi ▴ 10
Ah yes sorry :) But then I still do not understand why is it that on the plot I attached, the gene definitely has non-0 counts in less than…
Answer: Typo in the help of lmFit() by Gordon Smyth 52k
Thanks for the heads-up. > The _Details_ in the documentation of lmFit() still says that the default correlation is 0.75 Yes, you're righ…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by caroline.zanchi ▴ 10
Thank you ! ![enter image description here][1] In the end I did ```r rn2 <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "GENENAME"…
Answer: Memory issue while using "quickcluster" and "computeSumFactors" functions on sin by James W. MacDonald 68k
The obvious solution is to use cloud computing, which is likely cheaper than getting more RAM for your computer.
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
``` library(org.Dm.eg.db) rn <- select(org.Dm.eg.db, row.names(cent_expr_matrix), "SYMBOL","FLYBASE") ## ensure no NA values get propaga…
Votes
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
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