Showing : RNA-seq • reset
0
votes
2
replies
129
views
WGCNA less samples
RNA-Seq WGCNA Worms
13 days ago • updated 11 days ago davca • 0
0
votes
4
replies
326
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
9 weeks ago • updated 7 weeks ago ar14g12 • 0
0
votes
2
replies
3.1k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.4 years ago by ▴ 80
2
votes
3
replies
594
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 11 weeks ago by 49k • written 11 weeks ago by • 0
0
votes
3
replies
408
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 3 months ago by ★ 1.9k • written 3 months ago by • 0
3
votes
4
replies
584
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
3 months ago Eva ▴ 10
0
votes
3
replies
483
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 5 months ago by 41k • written 5 months ago by • 0
5
votes
7
replies
753
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 6 months ago by 49k • written 6 months ago by ▴ 10
0
votes
3
replies
513
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 6 months ago by 64k • written 6 months ago by • 0
0
votes
3
replies
559
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 6 months ago by 64k • written 6 months ago by • 0
1
vote
1
reply
725
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 7 months ago by ★ 3.6k • written 7 months ago by • 0
0
votes
1
reply
409
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 8 months ago by 64k • written 8 months ago by • 0
2
votes
2
replies
513
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 8 months ago by ★ 3.6k • written 8 months ago by • 0
0
votes
1
reply
439
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
9 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
552
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 12 months ago by 41k • written 12 months ago by • 0
5
votes
9
replies
1.5k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
16 months ago Yang Shi ▴ 10
2
votes
2
replies
927
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
16 months ago Yang Shi ▴ 10
0
votes
0
replies
682
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
16 months ago eolson • 0
2
votes
2
replies
737
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 16 months ago by 49k • written 16 months ago by • 0
0
votes
2
replies
1.7k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 3 months ago by • 0 • written 20 months ago by • 0
3
votes
3
replies
2.9k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 20 months ago by ▴ 30 • written 4.9 years ago by ▴ 30
5
votes
5
replies
1.4k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
21 months ago • updated 19 months ago 9906201a ▴ 20
1
vote
5
replies
1.6k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
22 months ago • updated 21 months ago Lucy ▴ 60
1
vote
3
replies
1.1k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 22 months ago by 41k • written 22 months ago by • 0
0
votes
5
replies
2.8k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 23 months ago by ★ 3.6k • written 2.7 years ago by • 0
0
votes
1
reply
777
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 23 months ago by 49k • written 23 months ago by • 0
1
vote
1
reply
2.2k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 2.3 years ago by ▴ 10 • written 3.4 years ago by ▴ 10
0
votes
5
replies
1.0k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.3 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
720
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.4 years ago lianov • 0
0
votes
1
reply
807
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.4 years ago • updated 2.3 years ago slcno • 0
3
votes
5
replies
2.2k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 2.5 years ago by 41k • written 2.5 years ago by ▴ 60
0
votes
1
reply
1.1k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 2.5 years ago by 3.9k • written 2.5 years ago by • 0
2
votes
3
replies
1.0k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.5 years ago by 49k • written 2.5 years ago by • 0
5
votes
2
replies
18k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 22 months ago by • 0 • written 4.9 years ago by ▴ 30
1
vote
1
reply
1.5k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 2.5 years ago by ★ 1.0k • written 2.5 years ago by ▴ 20
3
votes
4
replies
897
views
need help regarding differential expression analysis
rna-seq
updated 2.5 years ago by 3.9k • written 2.5 years ago by ▴ 20
0
votes
0
replies
768
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
2.6 years ago rbrns • 0
1
vote
4
replies
3.4k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 2.6 years ago by ★ 1.0k • written 6.2 years ago by • 0
3
votes
4
replies
1.2k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
2.6 years ago Antonio M. • 0
1
vote
2
replies
936
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 2.7 years ago by 49k • written 2.7 years ago by ▴ 20
1
vote
7
replies
1.2k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
2.7 years ago decppced • 0
1
vote
3
replies
739
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 2.7 years ago by 41k • written 2.7 years ago by • 0
0
votes
0
replies
770
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
2.9 years ago wrzl • 0
3
votes
9
replies
1.9k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
3.0 years ago Pufall, Miles A ▴ 30
0
votes
1
reply
831
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 3.0 years ago by 49k • written 3.0 years ago by • 0
0
votes
2
replies
1.2k
views
RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 3.0 years ago by 49k • written 3.0 years ago by ▴ 70
0
votes
2
replies
1.0k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 6 months ago by • 0 • written 3.1 years ago by • 0
3
votes
6
replies
2.5k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 2.8 years ago by 41k • written 3.1 years ago by ▴ 10
0
votes
3
replies
1.2k
views
GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 3.1 years ago by ★ 3.0k • written 3.1 years ago by ▴ 70
0
votes
3
replies
955
views
Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq DESeq2
updated 3.1 years ago by 41k • written 3.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Easiest way to convert read10xMolInfo data into a dataframe in R with gene label by Peter Hickey ▴ 650
An example usually helps. Here's a way to do it using base R. ``` library(DropletUtils) # Mocking up some 10X HDF5-formatted data. out <-…
Answer: rDGIdb package inconsistency with web interface by James W. MacDonald 64k
It doesn't appear to be inconsistent. Here is the [API call result][1]. And the [query on the old version][2]. Although as you may be notin…
Comment: Easiest way to convert read10xMolInfo data into a dataframe in R with gene label by Peter Hickey ▴ 650
Initially posted to https://github.com/MarioniLab/DropletUtils/issues/104
Comment: How to read fcs3.2 files by James W. MacDonald 64k
You need to supply more information than saying you tried things and they didn't work. Show code with error messages.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Looks good then.
Votes
Answer: SingleR annotation of several slots/patients
Answer: List of Deprecated Packages for Bioc3.18
Attempting to import SBML file using R
Answer: RNASeq time course analysis, missing time points for control
Answer: biomaRt not working - lazy table error
Awards • All
Popular Question to Henrik Bengtsson ★ 2.4k
Popular Question to paul.johnston ▴ 10
Teacher to Mike Smith ★ 6.2k
Popular Question to Bine ▴ 20
Popular Question to Robert Castelo ★ 3.0k
Locations • All
United States, 6 minutes ago
United States, 12 minutes ago
Canada, 13 minutes ago
Melbourne, Australia, 18 minutes ago
United States, 18 minutes ago
Traffic: 668 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6