Showing : rna-seq • reset
2
votes
4
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192
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 1 day ago by 42k • written 4 days ago by • 0
1
vote
2
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291
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
12 days ago • updated 11 days ago Dylan.Sheerin • 0
2
votes
3
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264
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 16 days ago by ★ 4.1k • written 18 days ago by • 0
3
votes
3
replies
371
views
permutation test in edgeR
rna-seq edgeR
updated 4 weeks ago by 50k • written 6 weeks ago by • 0
0
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2
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327
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WGCNA less samples
RNA-Seq WGCNA Worms
6 months ago • updated 5 months ago davca • 0
0
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4
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737
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
7 months ago ar14g12 • 0
2
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3
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1.7k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 8 months ago by 50k • written 8 months ago by • 0
0
votes
3
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699
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 8 months ago by ★ 1.9k • written 8 months ago by • 0
3
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4
replies
897
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
0
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3
replies
712
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 11 months ago by 42k • written 11 months ago by • 0
5
votes
7
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1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 12 months ago by 50k • written 12 months ago by ▴ 10
0
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3
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743
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 12 months ago by 66k • written 12 months ago by • 0
0
votes
3
replies
882
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 12 months ago by 66k • written 12 months ago by • 0
1
vote
1
reply
1.4k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
votes
1
reply
713
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 14 months ago by 66k • written 14 months ago by • 0
2
votes
2
replies
747
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 14 months ago by ★ 4.1k • written 14 months ago by • 0
0
votes
1
reply
687
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
15 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
742
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 18 months ago by 42k • written 18 months ago by • 0
5
votes
9
replies
1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
22 months ago Yang Shi ▴ 10
2
votes
2
replies
1.2k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
22 months ago Yang Shi ▴ 10
0
votes
0
replies
893
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
22 months ago eolson • 0
2
votes
2
replies
1.0k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 22 months ago by 50k • written 22 months ago by • 0
0
votes
2
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2.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 8 months ago by • 0 • written 2.1 years ago by • 0
5
votes
5
replies
1.6k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.2 years ago • updated 2.1 years ago 9906201a ▴ 20
1
vote
5
replies
2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.3 years ago Lucy ▴ 60
1
vote
3
replies
1.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
0
votes
1
reply
914
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.4 years ago by 50k • written 2.4 years ago by • 0
0
votes
5
replies
1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.8 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
931
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.8 years ago lianov • 0
0
votes
1
reply
1.0k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.8 years ago slcno • 0
3
votes
5
replies
2.6k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 2.9 years ago by 42k • written 2.9 years ago by ▴ 60
0
votes
1
reply
1.6k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by • 0
2
votes
3
replies
1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.0 years ago by 50k • written 3.0 years ago by • 0
1
vote
1
reply
1.7k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.0 years ago by ★ 1.0k • written 3.0 years ago by ▴ 20
3
votes
4
replies
1.1k
views
need help regarding differential expression analysis
rna-seq
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by ▴ 20
0
votes
0
replies
967
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.0 years ago rbrns • 0
3
votes
4
replies
1.4k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.1 years ago Antonio M. • 0
1
vote
2
replies
1.1k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 3.1 years ago by 50k • written 3.2 years ago by ▴ 20
0
votes
5
replies
3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.4 years ago by ★ 4.1k • written 3.2 years ago by • 0
1
vote
7
replies
1.4k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.2 years ago decppced • 0
1
vote
3
replies
859
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
0
votes
0
replies
889
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
3.3 years ago wrzl • 0
0
votes
1
reply
1.1k
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
3
votes
9
replies
2.2k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
3.5 years ago • updated 3.4 years ago Pufall, Miles A ▴ 30
0
votes
2
replies
1.6k
views
RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 3.5 years ago by 50k • written 3.5 years ago by ▴ 70
0
votes
2
replies
1.3k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 12 months ago by • 0 • written 3.5 years ago by • 0
3
votes
6
replies
3.0k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 3.3 years ago by 42k • written 3.6 years ago by ▴ 10
0
votes
3
replies
1.1k
views
Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq DESeq2
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
0
votes
0
replies
1.3k
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule microarray RNA-seq WGCNA
3.6 years ago modarzi ▴ 10
0
votes
0
replies
962
views
Job: Bioinformatics Developer / Computational Biologist
bioinformatics rna-seq shiny apps R algorithm development Job
3.6 years ago mmartin ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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