Showing : RNA-Seq • reset
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WGCNA: Problem with selecting soft threshold
biologicalnetworkanalysis genomes RNA-Seq co-expression wgcna
6 days ago Fernanda • 0
1
vote
3
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450
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 3 months ago by 67k • written 3 months ago by ▴ 50
2
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4
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581
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 4 months ago by 42k • written 4 months ago by • 0
1
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2
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523
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
4 months ago Dylan.Sheerin • 0
2
votes
5
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720
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 3 months ago by ★ 4.4k • written 4 months ago by • 0
3
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3
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680
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permutation test in edgeR
rna-seq edgeR
updated 5 months ago by 51k • written 5 months ago by • 0
0
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1
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1.1k
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Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 9 months ago by ★ 4.4k • written 6.4 years ago by • 0
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2
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477
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WGCNA less samples
RNA-Seq WGCNA Worms
10 months ago davca • 0
0
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4
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1.0k
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
12 months ago • updated 11 months ago ar14g12 • 0
0
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2
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4.0k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.2 years ago by ▴ 80
2
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3
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2.8k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 12 months ago by 51k • written 12 months ago by • 0
0
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3
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907
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 13 months ago by ★ 1.9k • written 13 months ago by • 0
3
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4
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1.1k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
13 months ago Eva ▴ 10
0
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3
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849
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 15 months ago by 42k • written 15 months ago by • 0
5
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7
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1.5k
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 16 months ago by 51k • written 16 months ago by ▴ 10
0
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3
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923
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization PCR_efficiency bias intrasample_comparison
updated 16 months ago by 67k • written 16 months ago by • 0
0
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3
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1.1k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 16 months ago by 67k • written 16 months ago by • 0
1
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1
reply
1.9k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 17 months ago by ★ 4.4k • written 17 months ago by • 0
0
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1
reply
887
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 18 months ago by 67k • written 18 months ago by • 0
2
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2
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950
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Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 18 months ago by ★ 4.4k • written 18 months ago by • 0
0
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1
reply
806
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
19 months ago Jenny Drnevich ★ 2.0k
0
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1
reply
922
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 22 months ago by 42k • written 22 months ago by • 0
5
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9
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2.2k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.2 years ago Yang Shi ▴ 10
2
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2
replies
1.4k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.2 years ago Yang Shi ▴ 10
0
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0
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1.0k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.2 years ago eolson • 0
2
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2
replies
1.2k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.2 years ago by 51k • written 2.2 years ago by • 0
0
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2
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2.9k
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Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 13 months ago by • 0 • written 2.5 years ago by • 0
3
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3
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3.7k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.5 years ago by ▴ 30 • written 5.7 years ago by ▴ 40
5
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5
replies
1.9k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.6 years ago • updated 2.4 years ago 9906201a ▴ 20
1
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5
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2.4k
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featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.6 years ago Lucy ▴ 60
1
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3
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1.6k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
0
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5
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4.3k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.7 years ago by ★ 4.4k • written 3.5 years ago by • 0
0
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1
reply
1.0k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.7 years ago by 51k • written 2.7 years ago by • 0
1
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1
reply
3.1k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 3.1 years ago by ▴ 10 • written 4.3 years ago by ▴ 10
0
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5
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1.5k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.1 years ago bioinformatic_trainee ▴ 10
0
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0
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1.0k
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.2 years ago lianov • 0
0
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1
reply
1.1k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.2 years ago • updated 3.1 years ago slcno • 0
3
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5
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3.1k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.3 years ago by 42k • written 3.3 years ago by ▴ 60
0
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1
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2.1k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.3 years ago by ★ 4.0k • written 3.3 years ago by • 0
2
votes
3
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1.4k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.3 years ago by 51k • written 3.3 years ago by • 0
5
votes
2
replies
24k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.7 years ago by ▴ 30
1
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1
reply
1.9k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.3 years ago by ★ 1.1k • written 3.3 years ago by ▴ 20
3
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4
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1.2k
views
need help regarding differential expression analysis
rna-seq
updated 3.4 years ago by ★ 4.0k • written 3.4 years ago by ▴ 20
0
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0
replies
1.1k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.4 years ago rbrns • 0
1
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4
replies
4.2k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.4 years ago by ★ 1.1k • written 7.0 years ago by • 0
3
votes
4
replies
1.6k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.4 years ago Antonio M. • 0
1
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2
replies
1.2k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 3.5 years ago by 51k • written 3.5 years ago by ▴ 20
1
vote
7
replies
1.6k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.5 years ago decppced • 0
1
vote
3
replies
955
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.6 years ago by 42k • written 3.6 years ago by • 0
0
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0
replies
1.0k
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
3.7 years ago wrzl • 0
50 results • Page 1 of 1
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Comment: How should I run ssGSEA Hallmark Enrichment Analysis? by Ginny • 0
I think the other side of this question is that the non protein coding genes would be in the "background", they would influence the ranking…
Comment: ISO a solution to rank-order introns by transcript by James W. MacDonald 67k
There's an error in the last line. Note that `sapply(lengths(z), seq_len)` will return a `list` because the lengths vary. We need a vector,…
Comment: BiomaRt - improved access to Ensembl ? by Mike Smith ★ 6.5k
Why do you want to use `useMart()` rather than `useEnsembl()`? They are essentially the same (`useEnsembl()` will eventually call `useMart(…
Comment: Installing Bioconductor packages in Docker by devarti.mahakalkar • 0
I have installed BiocManager on my base image rather than having it as base image. RUN Rscript -e "install.packages('BiocManager', re…
Comment: Meta-analysis on RNA-seq data sets by Travis • 0
Thank you for your suggestions and explanation of your approach!
Votes
Answer: ISO a solution to rank-order introns by transcript
Answer: ISO a solution to rank-order introns by transcript
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're c
Answer: addPatternDensity in 'qsea' takes too much time
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