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 7.4 years ago by ▴ 10
3
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4
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8.0k
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Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
written 5.3 years ago by ▴ 80
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1
reply
951
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To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 9 months ago by 53k • written 9 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 6.9 years ago by ▴ 30
1
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6
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1.6k
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 12 months ago by 43k • written 12 months ago by ▴ 10
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2
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690
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
13 months ago paul.meraner • 0
0
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0
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599
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
14 months ago Fernanda • 0
1
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3
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1.1k
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 17 months ago by 68k • written 17 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 18 months ago by 43k • written 18 months ago by • 0
1
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2
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1.1k
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
18 months ago Dylan.Sheerin • 0
2
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6
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2.3k
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 8 months ago by • 0 • written 19 months ago by • 0
3
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3
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1.8k
views
permutation test in edgeR
rna-seq edgeR
updated 19 months ago by 53k • written 19 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 23 months ago by ★ 5.0k • written 7.6 years ago by • 0
0
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2
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796
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WGCNA less samples
RNA-Seq WGCNA Worms
2.0 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
2.2 years ago • updated 2.1 years ago ar14g12 • 0
0
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2
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4.9k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.4 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 2.2 years ago by 53k • written 2.2 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 2.2 years ago by ★ 1.9k • written 2.2 years ago by • 0
3
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4
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2.0k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.3 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 2.4 years ago by 43k • written 2.5 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 2.5 years ago by 53k • written 2.5 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 2.5 years ago by 68k • written 2.5 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 2.5 years ago by 68k • written 2.5 years ago by • 0
1
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1
reply
3.2k
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FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by ▴ 10
0
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1
reply
1.6k
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
2
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2
replies
1.3k
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
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1
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1.2k
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
2.8 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 3.0 years ago by 43k • written 3.0 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
3.3 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
3.3 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
3.4 years ago eolson • 0
2
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2
replies
1.7k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 3.4 years ago by 53k • written 3.4 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 2.2 years ago by • 0 • written 3.6 years ago by • 0
3
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3
replies
4.8k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 3.7 years ago by ▴ 30 • written 6.8 years ago by ▴ 40
5
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5
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3.1k
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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
3.7 years ago • updated 3.6 years ago 9906201a ▴ 20
1
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5
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3.4k
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featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.8 years ago Lucy ▴ 60
1
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3
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2.2k
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Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 3.8 years ago by 43k • written 3.8 years ago by • 0
0
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5
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6.0k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 3.9 years ago by ★ 5.0k • written 4.7 years ago by • 0
0
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1
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1.4k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 3.9 years ago by 53k • written 3.9 years ago by • 0
1
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1
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3.9k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 4.3 years ago by ▴ 10 • written 5.4 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
4.3 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
4.3 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
4.3 years ago slcno • 0
3
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5
replies
4.3k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 4.4 years ago by 43k • written 4.5 years ago by ▴ 60
0
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1
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2.9k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 4.5 years ago by ★ 4.0k • written 4.5 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 4.5 years ago by 53k • written 4.5 years ago by • 0
1
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1
reply
2.4k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 4.5 years ago by ★ 1.1k • written 4.5 years ago by ▴ 20
3
votes
4
replies
1.6k
views
need help regarding differential expression analysis
rna-seq
updated 4.5 years ago by ★ 4.0k • written 4.5 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
4.5 years ago rbrns • 0
1
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4
replies
5.1k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 4.6 years ago by ★ 1.1k • written 8.2 years ago by • 0
418 results • Page 1 of 9
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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