Showing : RNA-Seq • reset
2
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40
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 54 minutes ago by 41k • written 1 hour ago by • 0
3
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3
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326
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permutation test in edgeR
rna-seq edgeR
updated 12 days ago by 50k • written 25 days ago by • 0
0
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2
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312
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WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
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4
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705
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
7 months ago • updated 6 months ago ar14g12 • 0
2
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3
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1.6k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
0
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3
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655
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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
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867
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
8 months ago Eva ▴ 10
0
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3
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683
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 10 months ago by 41k • written 10 months ago by • 0
5
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7
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1.2k
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 11 months ago by 50k • written 11 months ago by ▴ 10
0
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3
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712
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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 11 months ago by 65k • written 11 months ago by • 0
0
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3
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848
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Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 11 months ago by 65k • written 11 months ago by • 0
1
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1
reply
1.3k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
votes
1
reply
682
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Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 13 months ago by 65k • written 13 months ago by • 0
2
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2
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722
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Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
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1
reply
660
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Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
14 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
712
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Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 17 months ago by 41k • written 17 months ago by • 0
5
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9
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1.9k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
21 months ago Yang Shi ▴ 10
2
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2
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1.2k
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
21 months ago Yang Shi ▴ 10
0
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0
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863
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Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
21 months ago eolson • 0
2
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2
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974
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How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 21 months ago by 50k • written 21 months ago by • 0
0
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2
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2.3k
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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
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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 2.0 years ago 9906201a ▴ 20
1
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5
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2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
1
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3
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1.4k
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Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
0
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1
reply
893
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.3 years ago by 50k • written 2.3 years ago by • 0
0
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5
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1.2k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.7 years ago bioinformatic_trainee ▴ 10
0
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0
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909
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.8 years ago lianov • 0
0
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1
reply
1.0k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.8 years ago • updated 2.7 years ago slcno • 0
3
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5
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2.6k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 2.9 years ago by 41k • written 2.9 years ago by ▴ 60
0
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1
reply
1.6k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
2
votes
3
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1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.9 years ago by 50k • written 2.9 years ago by • 0
1
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1
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1.7k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 2.9 years ago by ★ 1.0k • written 2.9 years ago by ▴ 20
3
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4
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1.1k
views
need help regarding differential expression analysis
rna-seq
updated 2.9 years ago by ★ 3.9k • written 3.0 years ago by ▴ 20
0
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0
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941
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Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.0 years ago rbrns • 0
3
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4
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1.4k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.0 years ago Antonio M. • 0
1
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2
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1.1k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
0
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5
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3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.1k • written 3.1 years ago by • 0
1
vote
7
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1.4k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.1 years ago decppced • 0
1
vote
3
replies
842
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.1 years ago by 41k • written 3.1 years ago by • 0
0
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0
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871
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Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
3.3 years ago wrzl • 0
0
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1
reply
1.0k
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
3.4 years ago Pufall, Miles A ▴ 30
0
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2
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1.5k
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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
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2
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1.2k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 11 months ago by • 0 • written 3.5 years ago by • 0
3
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6
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2.9k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 3.2 years ago by 41k • written 3.5 years ago by ▴ 10
0
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3
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1.1k
views
Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq DESeq2
updated 3.5 years ago by 41k • written 3.5 years ago by • 0
0
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0
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1.3k
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule microarray RNA-seq WGCNA
3.5 years ago modarzi ▴ 10
0
votes
0
replies
938
views
Job: Bioinformatics Developer / Computational Biologist
bioinformatics rna-seq shiny apps R algorithm development Job
3.5 years ago mmartin ▴ 20
0
votes
3
replies
1.4k
views
GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 3.5 years ago by ★ 3.3k • written 3.6 years ago by ▴ 70
0
votes
0
replies
777
views
circRNAprofiler - miRNA binding sites
circRNA RNA-seq circRNAprofiler
3.6 years ago Terra • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Votes
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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