Showing : rnaseq • reset
1
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4
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3.1k
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Should I perform batch correction of normalized RNA-seq counts prior to GSVA?
GSVA GSVAdata RNAseq
19 months ago Lucy ▴ 60
0
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4
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1.2k
views
DE analysis in EdgeR /Can any one please help me.
RNASeqData DEGraph RNASeq edgeR DegNorm
written 19 months ago by • 0
0
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0
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827
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
20 months ago JG13 • 0
0
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1
reply
799
views
Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 20 months ago by 68k • written 20 months ago by • 0
1
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9
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4.2k
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 20 months ago by 68k • written 20 months ago by ▴ 10
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 20 months ago by 68k • written 20 months ago by ▴ 50
2
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2
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1.1k
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 21 months ago by ▴ 10 • written 21 months ago by • 0
0
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6
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2.5k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
21 months ago atan • 0
3
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2
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1.4k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
21 months ago mohammedtoufiq91 ▴ 10
0
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0
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727
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
21 months ago Bibi • 0
10
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11
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3.4k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 21 months ago by • 0 • written 8.5 years ago by ▴ 80
1
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3
replies
1.2k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
3
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1.9k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
0
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1
reply
949
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 22 months ago by 43k • written 22 months ago by • 0
0
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2
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871
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 22 months ago by • 0
0
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2
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1.4k
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
22 months ago catv • 0
5
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3
replies
1.8k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 21 months ago by 53k • written 22 months ago by • 0
0
votes
1
reply
1.7k
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 22 months ago by 43k • written 22 months ago by • 0
0
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1
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1.1k
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 22 months ago by ★ 5.0k • written 22 months ago by • 0
0
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2
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2.4k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
23 months ago kcarey • 0
2
votes
2
replies
938
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
23 months ago Sabiha ▴ 20
0
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2
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4.1k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
23 months ago kcarey • 0
1
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4
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1.0k
views
DESeq2 Replicates
DESeq2 RNASeq
23 months ago kcarey • 0
1
vote
3
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1.2k
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 24 months ago by ★ 1.4k • written 24 months ago by ▴ 10
0
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4
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1.1k
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
24 months ago mperalc • 0
0
votes
2
replies
1.3k
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 24 months ago by 53k • written 24 months ago by • 0
3
votes
5
replies
1.9k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 24 months ago by 43k • written 2.0 years ago by ▴ 10
2
votes
1
reply
819
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 24 months ago by 43k • written 24 months ago by ▴ 10
3
votes
7
replies
2.2k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
2.0 years ago • updated 5 months ago boczniak767 ▴ 740
0
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0
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847
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
2.0 years ago Abril • 0
2
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2
replies
1.9k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
2.0 years ago jackafiore • 0
1
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2
replies
2.7k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.8 years ago by • 0
0
votes
4
replies
1.1k
views
Ballgown error in scan for c.tab files
ballgown RNASeq
2.1 years ago candacenewcome • 0
1
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3
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1.3k
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
2.1 years ago island • 0
1
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3
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1.4k
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 2.1 years ago by • 0
0
votes
1
reply
722
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 2.1 years ago by ▴ 220 • written 2.1 years ago by • 0
2
votes
4
replies
3.2k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
2.1 years ago Sabiha ▴ 20
4
votes
6
replies
1.8k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 2.0 years ago by 53k • written 2.1 years ago by • 0
3
votes
1
reply
968
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
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3
replies
1.7k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 2.1 years ago by • 0
0
votes
1
reply
908
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
2.1 years ago WS • 0
2
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3
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4.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
1
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2
replies
1.4k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
2.2 years ago Sabiha ▴ 20
1
vote
2
replies
1.3k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
2.2 years ago drewhaydensteele • 0
12
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5
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5.7k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 8 months ago by • 0 • written 2.2 years ago by • 0
0
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3
replies
1.4k
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
2.3 years ago • updated 2.2 years ago Karthik • 0
1
vote
1
reply
883
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 2.2 years ago by 43k • written 2.3 years ago by • 0
2
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3
replies
1.7k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
2.3 years ago • updated 2.2 years ago Karthik • 0
2
votes
2
replies
1.2k
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
2.3 years ago Manthos • 0
2
votes
4
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1.6k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
2.3 years ago Tyler Sagendorf ▴ 10
1,414 results • Page 2 of 29
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Answer: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
I'm not familiar with the packages you mention, but the whole reason why Bioconductor has versions is that code and annotation change. Code…
Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Votes
Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
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