Showing : RNA-SEQ • reset
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problem for finding soft power for constructing network in WGCNA algorithm
RNA-seq WGCNA package soft power
written 7.2 years ago by ▴ 10
3
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4
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7.9k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.2 years ago by ▴ 80
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1
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891
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 7 months ago by 53k • written 7 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 6.7 years ago by ▴ 30
1
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6
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1.5k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 10 months ago by 43k • written 10 months ago by ▴ 10
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2
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611
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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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561
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
12 months ago Fernanda • 0
1
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3
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936
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 15 months ago by 68k • written 15 months ago by ▴ 50
2
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4
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1.0k
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 16 months ago by 43k • written 16 months ago by • 0
1
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2
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987
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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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2.1k
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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
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1.7k
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permutation test in edgeR
rna-seq edgeR
updated 17 months ago by 53k • written 18 months ago by • 0
0
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1
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1.3k
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 21 months ago by ★ 4.9k • written 7.5 years ago by • 0
0
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2
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754
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WGCNA less samples
RNA-Seq WGCNA Worms
22 months ago davca • 0
0
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4
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1.4k
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
2.0 years ago • updated 23 months ago ar14g12 • 0
0
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2
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4.8k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.2 years ago by ▴ 80
2
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3
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4.7k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 2.0 years ago by 53k • written 2.1 years ago by • 0
0
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3
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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
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4
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1.9k
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 2.3 years ago by 43k • written 2.3 years ago by • 0
5
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7
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2.1k
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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1.4k
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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
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1
reply
3.1k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 2.5 years ago by ★ 4.9k • written 2.5 years ago by ▴ 10
0
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1
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1.5k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
2
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2
replies
1.3k
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 2.5 years ago by ★ 4.9k • written 2.5 years ago by • 0
0
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1
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1.1k
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
2.6 years ago Jenny Drnevich ★ 2.0k
0
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1
reply
1.2k
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 2.8 years ago by 43k • written 2.9 years ago by • 0
5
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9
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2.9k
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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
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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
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1.3k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
3.2 years ago eolson • 0
2
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2
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1.6k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
0
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2
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4.1k
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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
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3
replies
4.7k
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Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.5 years ago by ▴ 30 • written 6.7 years ago by ▴ 40
5
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5
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3.0k
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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
3.6 years ago • updated 3.4 years ago 9906201a ▴ 20
1
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5
replies
3.3k
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featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.6 years ago Lucy ▴ 60
1
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3
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2.1k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 3.6 years ago by 43k • written 3.6 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 3.7 years ago by ★ 4.9k • written 4.5 years ago by • 0
0
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1
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1.3k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
1
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1
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3.8k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 4.1 years ago by ▴ 10 • written 5.3 years ago by ▴ 10
0
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5
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1.9k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
4.1 years ago bioinformatic_trainee ▴ 10
0
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0
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1.3k
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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
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1.4k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
4.2 years ago • updated 4.1 years ago slcno • 0
3
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5
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4.2k
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Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 4.3 years ago by 43k • written 4.3 years ago by ▴ 60
0
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1
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2.9k
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Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 4.3 years ago by ★ 4.0k • written 4.3 years ago by • 0
2
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3
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1.8k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 4.3 years ago by 53k • written 4.4 years ago by • 0
1
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1
reply
2.3k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 4.3 years ago by ★ 1.1k • written 4.4 years ago by ▴ 20
3
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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
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1.3k
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
4.9k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4.5 years ago by ★ 1.1k • written 8.0 years ago by • 0
418 results • Page 1 of 9
Recent ...
Replies
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
Comment: incomplete imputation of missing values with LEA impute() function by Gordon Smyth 53k
Nadia, please tag your question with the name of the package ("LEA") that you are asking about. "impute" is the name of a different Biocond…
Comment: Sharing a collection of datasets in ExperimentHub by Aaron Lun ★ 29k
FYI the **scRNAseq** packages uses a non-ExperimentHub storage platform, see [here](https://github.com/ArtifactDB/gypsum-worker) for more d…
Comment: Error Loading Experiment from SimBenchData Package by ATpoint ★ 4.9k
Is the Seurat package installed? The error somewhat suggests that it could be related, and at https://www.bioconductor.org/packages/release…
Votes
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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