Showing : RNA-Seq • reset
0
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1.5k
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problem for finding soft power for constructing network in WGCNA algorithm
RNA-seq WGCNA package soft power
written 7.5 years ago by ▴ 10
3
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4
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8.4k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.5 years ago by ▴ 80
0
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1
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1.1k
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 11 months ago by 53k • written 11 months ago by ▴ 80
5
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3
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29k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 7.0 years ago by ▴ 30
1
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6
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1.7k
views
Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 14 months ago by 43k • written 14 months ago by ▴ 10
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2
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758
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
15 months ago paul.meraner • 0
0
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0
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652
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
16 months ago Fernanda • 0
1
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3
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1.1k
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 19 months ago by 68k • written 19 months ago by ▴ 50
2
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4
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1.2k
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 20 months ago by 43k • written 20 months ago by • 0
1
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2
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1.2k
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
20 months ago Dylan.Sheerin • 0
2
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6
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2.6k
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 11 months ago by • 0 • written 21 months ago by • 0
3
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3
replies
2.0k
views
permutation test in edgeR
rna-seq edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
0
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1
reply
1.5k
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 2.1 years ago by ★ 5.0k • written 7.8 years ago by • 0
0
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2
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876
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WGCNA less samples
RNA-Seq WGCNA Worms
2.2 years ago davca • 0
0
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4
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1.5k
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
2.3 years ago ar14g12 • 0
0
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2
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5.2k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.5 years ago by ▴ 80
2
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3
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5.3k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
0
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3
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1.4k
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by • 0
3
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4
replies
2.3k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.5 years ago Eva ▴ 10
0
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3
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1.3k
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 2.6 years ago by 43k • written 2.6 years ago by • 0
5
votes
7
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2.4k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 2.7 years ago by 53k • written 2.7 years ago by ▴ 10
0
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3
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1.4k
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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 2.7 years ago by 68k • written 2.7 years ago by • 0
0
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3
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1.6k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
1
vote
1
reply
3.3k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 10
0
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1
reply
1.7k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
2
votes
2
replies
1.4k
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 2.8 years ago by ★ 5.0k • written 2.9 years ago by • 0
0
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1
reply
1.2k
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
3.0 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 3.2 years ago by 43k • written 3.2 years ago by • 0
5
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9
replies
3.2k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
3.5 years ago Yang Shi ▴ 10
2
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2
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2.1k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
3.5 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
3.5 years ago eolson • 0
2
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2
replies
1.8k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 3.5 years ago by 53k • written 3.5 years ago by • 0
0
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2
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4.3k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 2.4 years ago by • 0 • written 3.8 years ago by • 0
3
votes
3
replies
5.0k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.9 years ago by ▴ 30 • written 7.0 years ago by ▴ 40
5
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5
replies
3.2k
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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
3.9 years ago • updated 3.7 years ago 9906201a ▴ 20
1
vote
5
replies
3.5k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
4.0 years ago • updated 3.9 years ago Lucy ▴ 60
1
vote
3
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2.3k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
0
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5
replies
6.3k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 4.0 years ago by ★ 5.0k • written 4.8 years ago by • 0
0
votes
1
reply
1.5k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 4.0 years ago by 53k • written 4.0 years ago by • 0
1
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1
reply
4.2k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 4.4 years ago by ▴ 10 • written 5.6 years ago by ▴ 10
0
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5
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2.1k
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DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
4.5 years ago bioinformatic_trainee ▴ 10
0
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0
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1.4k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
4.5 years ago lianov • 0
0
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1
reply
1.6k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
4.5 years ago slcno • 0
3
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5
replies
4.8k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 60
0
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1
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3.1k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by • 0
2
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3
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1.9k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 4.7 years ago by 53k • written 4.7 years ago by • 0
1
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1
reply
2.5k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 4.7 years ago by ★ 1.1k • written 4.7 years ago by ▴ 20
3
votes
4
replies
1.7k
views
need help regarding differential expression analysis
rna-seq
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 20
0
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0
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1.4k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
4.7 years ago rbrns • 0
1
vote
4
replies
5.2k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4.8 years ago by ★ 1.1k • written 8.3 years ago by • 0
418 results • Page 1 of 9
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Replies
Answer: Confirm that OpenStats will not be archived (pryr dependency) by shepherl 4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Michael Love 43k
Yes, I find that the LFC shrinkage and its corresponding stat `svalue` if you use lfcShrink with a threshold often returns more reliable ge…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Federico Marini ▴ 180
Jumping in on this - all this started because we want to "do it right", i.e. avoiding the post-hoc filtering on the logFC (which is still w…
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Michael Love 43k
it looks above like you have a gene with two non-zero count samples. Also, yes you can use a stricter filter. You cannot estimate the LFC …
Comment: Lowly expressed genes reported as significant when using lfcThreshold in DESeq by Ahmed Salah • 0
Thank you very much for your answer. Actually, this is after pre-filtering ```r keep <- rowSums(counts(dds) >= 10) >= 3 dds <- dds[keep, …
Votes
Answer: Limpa Pipeline Order
Answer: Array weights in dpcDE
Answer: Array weights in dpcDE
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
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