Showing : RNASeqR • reset
6
votes
11
replies
3.9k
views
How to properly average normalized counts of biological replicates
DESeq2 Normalization RNASeqR
updated 5 weeks ago by • 0 • written 3.1 years ago by ▴ 40
0
votes
2
replies
2.2k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 7 months ago by • 0 • written 2.0 years ago by • 0
0
votes
1
reply
942
views
Batch effects in DESeq2: determination and model building
BatchEffect batch RNASeqR formula DESeq2
updated 20 months ago by 41k • written 20 months ago by • 0
0
votes
3
replies
1.3k
views
using of z score in Differentially Expression Analysis
RNASeqR
updated 20 months ago by ★ 4.0k • written 20 months ago by • 0
1
vote
1
reply
775
views
edgeR for SDE analysis
RNASeqRData edgeR RNASeqR RNASeqData
updated 2.1 years ago by 50k • written 2.2 years ago by • 0
1
vote
3
replies
1.2k
views
Error with hclust
RNASeqR #hclust #wgcna #dissimilarity #average
updated 2.4 years ago by ★ 4.0k • written 2.4 years ago by • 0
4
votes
1
reply
1.9k
views
mitochondrial RNA percentage in bulk RNAseq data
rnaseqGene RNASeqR DESeq2 RNAseq
updated 2.5 years ago by 41k • written 2.5 years ago by ▴ 10
0
votes
1
reply
823
views
Question about normalizing and removing batch effects from bulk RNA-seq data from NCBI-SRA
Arabidopsis_thaliana_Data RNASeqR Normalization BatchEffect
updated 2.5 years ago by 65k • written 2.5 years ago by ▴ 20
0
votes
1
reply
908
views
Outliers on DESEq2 Results
RNASeqR DifferentialExpression DESeq2
updated 2.6 years ago by 41k • written 2.6 years ago by • 0
1
vote
10
replies
2.9k
views
Duplicate correlation with limma in before-after exposure experiment
RNASeqR
3.4 years ago • updated 3.0 years ago sofie.haglund • 0
2
votes
2
replies
1.4k
views
Need help in determing upregulated and downregulated genes
RNASeqR
3.0 years ago Rishav ▴ 20
1
vote
3
replies
1.7k
views
Mapping EntrezId to Ensembl IDs returns NA for pseudogenes and snoRNA
RNASeqData RNASeq RNASeqR
3.0 years ago dantasezequiel1 • 0
3
votes
4
replies
1.3k
views
GEO + RNA-seq. Total Newbie.
RNASeqData RNASeq GEO RNASeqR HELP
3.0 years ago hgalmoore • 0
0
votes
1
reply
854
views
Limma Voom Design and Contrast Matrix- Can my parameter also be a factor?
RNASeqRData limma RNASeq RNASeqR
updated 3.0 years ago by 50k • written 3.0 years ago by • 0
1
vote
5
replies
1.6k
views
while designing matrix i got an error, please help me out
RNASeqR
updated 3.1 years ago by ▴ 770 • written 3.1 years ago by ▴ 20
1
vote
2
replies
824
views
Bioconductor packages for doing tRNA seq analysis
RNASeqR
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
1
vote
3
replies
874
views
Need help in doing network analysis using R
RNASeqR
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by ▴ 20
1
vote
2
replies
821
views
Error occured in designing a matrix
RNASeqR
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
1
vote
5
replies
868
views
Error when calculating DE using the classical approach in edgeR
RNASeqR
3.1 years ago Rishav ▴ 20
1
vote
2
replies
1.4k
views
I am creating contrast matrix and i am following every procedure but still i don't understand where i am getting error
RNASeqR
3.1 years ago Rishav ▴ 20
0
votes
1
reply
2.2k
views
Biological replicates in DESeq2
DESeq2 Bioconductor RNASeqR
updated 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
votes
1
reply
1.0k
views
Using tximport to create the input for DESeq2
RNASeqR
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
5
votes
5
replies
2.4k
views
analyzing RNA-Seq transcriptomic data (GEO accession: GSE96058)
GEO RNASeqR Transcriptomics
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 10
0
votes
2
replies
5.2k
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
3.2 years ago RJM • 0
0
votes
1
reply
739
views
Find significant genes related to a specific disease
GeneExpression RNASeqR limma
updated 3.4 years ago by ▴ 490 • written 3.4 years ago by • 0
7
votes
6
replies
3.4k
views
WHat is the difference between DEG and TopVarGenes in DESEq2?
DESeq2 R RNASeqR
3.4 years ago ecg1g15 ▴ 20
3
votes
5
replies
2.0k
views
Volcano plot - select additional gene
EnhancedVolcano RNASeqR R volcanoplot
updated 3.5 years ago by ★ 3.9k • written 3.5 years ago by ▴ 10
27 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Fair enough, I guess it depends on the comparison being made, right? If one was interested in a feature comparing Timepoint A vs B, then it…
Comment: DESeq2 setting significant p-value by Dev • 0
Sir but when I put in the expression data via the csv file, it was showing the gene names then but now when i set it in the form factor it …
Answer: OrgDb for maize by James W. MacDonald 65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Awards • All
Popular Question to shepherl 3.8k
Popular Question to BioinfGuru ▴ 30
Popular Question to Gordon Smyth 50k
Scholar to Peter Hickey ▴ 740
Popular Question to sropri • 0
Locations • All
Germany, 1 minute ago
United States, 1 minute ago
India, 1 minute ago
France, 7 minutes ago
France, 18 minutes ago
Traffic: 861 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6