Showing : RNA-SEQ • reset
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
6 hours ago paul.meraner • 0
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0
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92
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
13 days ago Fernanda • 0
1
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3
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461
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 3 months ago by 67k • written 3 months ago by ▴ 50
2
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4
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590
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 4 months ago by 42k • written 4 months ago by • 0
1
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2
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530
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
4 months ago Dylan.Sheerin • 0
2
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5
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745
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 3 months ago by ★ 4.5k • written 5 months ago by • 0
3
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3
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698
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permutation test in edgeR
rna-seq edgeR
updated 5 months ago by 51k • written 5 months ago by • 0
0
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1
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1.1k
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 9 months ago by ★ 4.5k • written 6.5 years ago by • 0
0
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2
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484
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WGCNA less samples
RNA-Seq WGCNA Worms
10 months ago davca • 0
0
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4
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1.0k
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
12 months ago • updated 11 months ago ar14g12 • 0
0
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2
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4.0k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.2 years ago by ▴ 80
2
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3
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2.9k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 12 months ago by 51k • written 12 months ago by • 0
0
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3
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919
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 13 months ago by ★ 1.9k • written 13 months ago by • 0
3
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4
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1.1k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
14 months ago Eva ▴ 10
0
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3
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857
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 15 months ago by 42k • written 15 months ago by • 0
5
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7
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1.5k
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 16 months ago by 51k • written 16 months ago by ▴ 10
0
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3
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937
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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 17 months ago by 67k • written 17 months ago by • 0
0
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3
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1.1k
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Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 17 months ago by 67k • written 17 months ago by • 0
1
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1
reply
2.0k
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FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 17 months ago by ★ 4.5k • written 17 months ago by • 0
0
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1
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894
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Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 18 months ago by 67k • written 18 months ago by • 0
2
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2
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959
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Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 18 months ago by ★ 4.5k • written 18 months ago by • 0
0
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1
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809
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
20 months ago • updated 19 months ago Jenny Drnevich ★ 2.0k
0
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1
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938
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Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 22 months ago by 42k • written 22 months ago by • 0
5
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9
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2.2k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.2 years ago Yang Shi ▴ 10
2
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2
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1.4k
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.2 years ago Yang Shi ▴ 10
0
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0
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1.0k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.2 years ago eolson • 0
2
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2
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1.2k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.2 years ago by 51k • written 2.2 years ago by • 0
0
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2
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2.9k
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Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 13 months ago by • 0 • written 2.5 years ago by • 0
3
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3
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3.8k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.6 years ago by ▴ 30 • written 5.7 years ago by ▴ 40
5
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5
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1.9k
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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
2.6 years ago • updated 2.4 years ago 9906201a ▴ 20
1
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5
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2.4k
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featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.6 years ago Lucy ▴ 60
1
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3
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1.6k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.6 years ago by 42k • written 2.7 years ago by • 0
0
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5
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4.3k
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.7 years ago by ★ 4.5k • written 3.5 years ago by • 0
0
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1
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1.0k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.7 years ago by 51k • written 2.7 years ago by • 0
1
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1
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3.1k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 3.1 years ago by ▴ 10 • written 4.3 years ago by ▴ 10
0
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5
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1.5k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.2 years ago • updated 3.1 years ago bioinformatic_trainee ▴ 10
0
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0
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1.0k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.2 years ago lianov • 0
0
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1
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1.2k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.2 years ago • updated 3.1 years ago slcno • 0
3
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5
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3.1k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.3 years ago by 42k • written 3.3 years ago by ▴ 60
0
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1
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2.1k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.3 years ago by ★ 4.0k • written 3.3 years ago by • 0
2
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3
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1.4k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.4 years ago by 51k • written 3.4 years ago by • 0
5
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2
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24k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.7 years ago by ▴ 30
1
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1
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1.9k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.3 years ago by ★ 1.1k • written 3.4 years ago by ▴ 20
3
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4
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1.2k
views
need help regarding differential expression analysis
rna-seq
updated 3.4 years ago by ★ 4.0k • written 3.4 years ago by ▴ 20
0
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0
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1.1k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.4 years ago rbrns • 0
1
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4
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4.2k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.5 years ago by ★ 1.1k • written 7.0 years ago by • 0
3
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4
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1.6k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.5 years ago Antonio M. • 0
1
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2
replies
1.2k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 3.5 years ago by 51k • written 3.5 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
3.6 years ago decppced • 0
1
vote
3
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962
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
50 results • Page 1 of 1
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Comment: miRTarRnaseq library by mercedeh.movassagh ▴ 20
Hi Maria, so what is the code you are using? By the 3rd way to conduct the analysis do you mean looking at the interaction model from part …
Comment: miRTarRnaseq library by María Calvo • 0
Hello, in line with the previous questions, when the miRNA-mRNA interaction analysis is performed (3 rd way to conduct the analysis), I obt…
Answer: heatmap with batch effect by James W. MacDonald 67k
You have only one condition in the second batch, so it's not possible to remove the batch effect. You can probably adjust for it somewhat, …
Answer: how do I convert an Ilumn IDREF to a CPG loci by James W. MacDonald 67k
``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame with 865859 rows and 3 columns ch…
Answer: Which input data is acceptable for MAST? by Andrew_McDavid ▴ 270
Not too familiar with SCT v2. If it also has a point-mass at zero and the non-zero component is roughly-symmetric, then it might work ok w…
Votes
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Comment: Convert HGVS Representation back to Reference Genome Coordinates
Answer: How to control batch effect if Group and batch are same?
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