Showing : RNA-Seq • reset
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Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis
deseq2 random effects batch effects RNA-seq rna-seq
updated 5 days ago by • 0 • written 7.8 years ago by • 0
3
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3
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7.4k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 16 days ago by • 0 • written 4.7 years ago by ▴ 80
5
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3
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2.6k
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single-cells RNA-seq analysis by MAST with unbalanced group size
mast single-cell rna-seq differential analysis
updated 29 days ago by ▴ 10 • written 7.3 years ago by ▴ 100
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2
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4.5k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.8 years ago by ▴ 80
5
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3
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28k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.3 years ago by ▴ 30
2
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6
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1.7k
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 8 weeks ago by • 0 • written 12 months ago by • 0
0
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1
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628
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 10 weeks ago by 52k • written 10 weeks ago by ▴ 80
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6
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1.3k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 5 months ago by 43k • written 5 months ago by ▴ 10
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2
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486
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
6 months ago paul.meraner • 0
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0
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387
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
7 months ago Fernanda • 0
1
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3
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776
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 10 months ago by 68k • written 10 months ago by ▴ 50
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1
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1.1k
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How to arrange multiple plots into one page in NOISeq?
noiseq RNA-seq quality control
updated 11 months ago by • 0 • written 5.7 years ago by ▴ 80
2
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4
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859
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 11 months ago by 43k • written 11 months ago by • 0
1
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2
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832
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
11 months ago Dylan.Sheerin • 0
3
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3
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1.4k
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permutation test in edgeR
rna-seq edgeR
updated 12 months ago by 52k • written 12 months ago by • 0
9
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12
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8.9k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 12 months ago by • 0 • written 9.8 years ago by ▴ 30
0
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1
reply
1.2k
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 16 months ago by ★ 4.8k • written 7.0 years ago by • 0
0
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2
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625
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WGCNA less samples
RNA-Seq WGCNA Worms
17 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 • updated 18 months ago ar14g12 • 0
2
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3
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4.3k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 19 months ago by 52k • written 19 months ago by • 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
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2
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3.8k
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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
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4
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1.6k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
21 months ago Eva ▴ 10
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10
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2.9k
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Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR rna-seq splice-variants
written 6.1 years ago by • 0
0
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3
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1.0k
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 22 months ago by 43k • written 22 months ago by • 0
5
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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 23 months ago by 52k • written 23 months ago by ▴ 10
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2
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1.6k
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Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 23 months ago by • 0 • written 4.5 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 23 months ago by 68k • written 23 months ago by • 0
0
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3
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1.1k
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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 23 months ago by 68k • written 23 months ago by • 0
1
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1
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2.9k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 2.0 years ago by ★ 4.8k • written 2.0 years ago by ▴ 10
0
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1
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1.3k
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Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
2
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2
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1.2k
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Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 2.1 years ago by ★ 4.8k • written 2.1 years ago by • 0
0
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1
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954
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
2.2 years ago Jenny Drnevich ★ 2.0k
1
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4
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1.4k
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Nested paired design with covariates in limma
RNA-seq Nested paired design limma
updated 2.2 years ago by 52k • written 5.1 years ago by • 0
4
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8
replies
3.0k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 2.2 years ago by 68k • written 4.9 years ago by ▴ 30
0
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1
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1.1k
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Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
6
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6
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7.6k
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strange results with featureCounts
RNA-seq featureCounts total RNA
updated 2.5 years ago by ▴ 200 • written 7.0 years ago by ▴ 10
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9
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2.7k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.8 years ago Yang Shi ▴ 10
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2
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1.7k
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How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.8 years ago Yang Shi ▴ 10
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0
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1.2k
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Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.8 years ago eolson • 0
2
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2
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1.4k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
5
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5
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2.6k
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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
3.2 years ago • updated 3.0 years ago 9906201a ▴ 20
3
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3
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4.4k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.1 years ago by ▴ 30 • written 6.3 years ago by ▴ 40
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2
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4.2k
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Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 3.2 years ago by • 0 • written 7.2 years ago by • 0
1
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5
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3.0k
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featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.2 years ago Lucy ▴ 60
1
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3
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1.9k
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Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 3.2 years ago by 43k • written 3.2 years ago by • 0
0
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5
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5.4k
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How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.3 years ago by ★ 4.8k • written 4.1 years ago by • 0
0
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1
reply
1.2k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 3.3 years ago by 52k • written 3.3 years ago by • 0
0
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7
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2.9k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 3.5 years ago by • 0 • written 7.9 years ago by ▴ 40
5
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12
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6.5k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 3.5 years ago by ▴ 30 • written 7.6 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2 by Tom • 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq by caroline.zanchi • 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Votes
Comment: Filtering after DESeq
A: Normalized counts from DESeq2 results in similar but not equal total read count?
A: DESeq2: Different Dispersions for different sample groups
A: Contrasts & coefficients in limma
Answer: How to formulate 2 factor nested design in DESeq2
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