Showing : RNA-Seq • reset
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1.4k
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problem for finding soft power for constructing network in WGCNA algorithm
RNA-seq WGCNA package soft power
written 7.3 years ago by ▴ 10
3
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4
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7.9k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.2 years ago by ▴ 80
0
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1
reply
912
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 8 months ago by 53k • written 8 months ago by ▴ 80
5
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3
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29k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.8 years ago by ▴ 30
1
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6
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1.5k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 11 months ago by 43k • written 11 months ago by ▴ 10
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2
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627
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
12 months ago paul.meraner • 0
0
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0
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573
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
13 months ago Fernanda • 0
1
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3
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949
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 16 months ago by 68k • written 16 months ago by ▴ 50
2
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4
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1.1k
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 17 months ago by 43k • written 17 months ago by • 0
1
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2
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1.0k
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
17 months ago Dylan.Sheerin • 0
2
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6
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2.2k
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 7 months ago by • 0 • written 17 months ago by • 0
3
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3
replies
1.7k
views
permutation test in edgeR
rna-seq edgeR
updated 18 months ago by 53k • written 18 months ago by • 0
0
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1
reply
1.4k
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 22 months ago by ★ 5.0k • written 7.5 years ago by • 0
0
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2
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766
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WGCNA less samples
RNA-Seq WGCNA Worms
23 months ago davca • 0
0
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4
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1.4k
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
2.1 years ago • updated 2.0 years ago ar14g12 • 0
0
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2
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4.8k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.3 years ago by ▴ 80
2
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3
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4.8k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
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3
replies
1.3k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 2.1 years ago by ★ 1.9k • written 2.1 years ago by • 0
3
votes
4
replies
2.0k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.2 years ago Eva ▴ 10
0
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3
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1.2k
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
5
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7
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2.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
0
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3
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1.3k
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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 2.4 years ago by 68k • written 2.4 years ago by • 0
0
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3
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1.5k
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Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
1
vote
1
reply
3.2k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by ▴ 10
0
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1
reply
1.5k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 2.6 years ago by 68k • written 2.6 years ago by • 0
2
votes
2
replies
1.3k
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
0
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1
reply
1.1k
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
2.7 years ago Jenny Drnevich ★ 2.0k
0
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1
reply
1.3k
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
5
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9
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3.0k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
3.2 years ago Yang Shi ▴ 10
2
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2
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2.0k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
3.2 years ago Yang Shi ▴ 10
0
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0
replies
1.3k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
3.3 years ago eolson • 0
2
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2
replies
1.6k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
0
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2
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4.1k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 2.1 years ago by • 0 • written 3.5 years ago by • 0
3
votes
3
replies
4.7k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.6 years ago by ▴ 30 • written 6.7 years ago by ▴ 40
5
votes
5
replies
3.0k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
3.6 years ago • updated 3.5 years ago 9906201a ▴ 20
1
vote
5
replies
3.3k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.7 years ago Lucy ▴ 60
1
vote
3
replies
2.2k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 3.7 years ago by 43k • written 3.7 years ago by • 0
0
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5
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5.9k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.8 years ago by ★ 5.0k • written 4.6 years ago by • 0
0
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1
reply
1.3k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 3.8 years ago by 53k • written 3.8 years ago by • 0
1
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1
reply
3.9k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 4.2 years ago by ▴ 10 • written 5.3 years ago by ▴ 10
0
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5
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1.9k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
4.2 years ago bioinformatic_trainee ▴ 10
0
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0
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1.3k
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
4.2 years ago lianov • 0
0
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1
reply
1.5k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
4.2 years ago slcno • 0
3
votes
5
replies
4.2k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 60
0
votes
1
reply
2.9k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by • 0
2
votes
3
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1.8k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 4.4 years ago by 53k • written 4.4 years ago by • 0
1
vote
1
reply
2.3k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 4.4 years ago by ★ 1.1k • written 4.4 years ago by ▴ 20
3
votes
4
replies
1.6k
views
need help regarding differential expression analysis
rna-seq
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by ▴ 20
0
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0
replies
1.4k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
4.4 years ago rbrns • 0
1
vote
4
replies
5.0k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4.5 years ago by ★ 1.1k • written 8.1 years ago by • 0
418 results • Page 1 of 9
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry by teamardigen • 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
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Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
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