Showing : RNASEQ • reset
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 19 months ago by 68k • written 19 months ago by • 0
1
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9
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3.7k
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 19 months ago by 68k • written 19 months ago by ▴ 10
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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 19 months ago by 68k • written 19 months ago by ▴ 50
2
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2
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1.1k
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 19 months ago by ▴ 10 • written 20 months ago by • 0
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6
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2.3k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
19 months ago atan • 0
3
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2
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1.3k
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
20 months ago mohammedtoufiq91 ▴ 10
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676
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
20 months ago Bibi • 0
10
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11
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3.3k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 20 months ago by • 0 • written 8.4 years ago by ▴ 80
1
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3
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1.1k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 20 months ago by 53k • written 20 months ago by • 0
0
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3
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1.5k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
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1
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895
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 20 months ago by 43k • written 20 months ago by • 0
0
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2
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837
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 21 months ago by • 0
0
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2
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1.3k
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
21 months ago catv • 0
5
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3
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1.6k
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Log-cpm values from limma
limma edgeR RNASeq
updated 20 months ago by 53k • written 21 months ago by • 0
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1
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1.4k
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 21 months ago by 43k • written 21 months ago by • 0
0
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1
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1.0k
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
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2
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2.1k
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
22 months ago kcarey • 0
2
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2
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898
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
22 months ago Sabiha ▴ 20
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2
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3.5k
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
22 months ago kcarey • 0
1
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4
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952
views
DESeq2 Replicates
DESeq2 RNASeq
22 months ago kcarey • 0
1
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3
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1.2k
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 22 months ago by ★ 1.4k • written 22 months ago by ▴ 10
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4
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1.1k
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
22 months ago mperalc • 0
0
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2
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1.2k
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Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 22 months ago by 53k • written 22 months ago by • 0
3
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5
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1.8k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 22 months ago by 43k • written 22 months ago by ▴ 10
2
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1
reply
781
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 22 months ago by 43k • written 22 months ago by ▴ 10
3
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7
replies
2.0k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
23 months ago • updated 4 months ago boczniak767 ▴ 740
0
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0
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793
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
23 months ago Abril • 0
2
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2
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1.8k
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
23 months ago jackafiore • 0
1
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2
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2.5k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.7 years ago by • 0
0
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4
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1.1k
views
Ballgown error in scan for c.tab files
ballgown RNASeq
23 months 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
23 months ago island • 0
1
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3
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1.4k
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 23 months ago by • 0
0
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1
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696
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 24 months ago by ▴ 220 • written 24 months ago by • 0
2
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4
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2.5k
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
24 months ago Sabiha ▴ 20
4
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6
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1.7k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 23 months ago by 53k • written 2.0 years ago by • 0
3
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1
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942
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
0
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3
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1.6k
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dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 2.0 years ago by • 0
0
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1
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861
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
2.0 years ago WS • 0
2
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3
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3.8k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
1
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2
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1.3k
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
2.1 years ago Sabiha ▴ 20
1
vote
2
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1.2k
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
2.1 years ago drewhaydensteele • 0
12
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5
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5.3k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 7 months ago by • 0 • written 2.1 years ago by • 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
2.1 years ago Karthik • 0
1
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1
reply
803
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
2
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3
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1.6k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
2.1 years ago Karthik • 0
2
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2
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1.1k
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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
2.1 years ago Manthos • 0
2
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4
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1.5k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
2.2 years ago Tyler Sagendorf ▴ 10
0
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1
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865
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 2.2 years ago by 43k • written 2.2 years ago by • 0
0
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2
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1.4k
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TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 2.2 years ago by ★ 1.1k • written 2.2 years ago by ▴ 200
0
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9
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3.3k
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DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 2.2 years ago by • 0 • written 8.2 years ago by ▴ 60
1,411 results • Page 2 of 29
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Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Have you told featureCounts to do strand-specific counting? As pointed out by Frances Turner, you can lose reads if they overlap the gene …
Answer: Clarification on counting in Rsubread (featureCounts) by Frances Turner ▴ 10
You should look at the summary files produced by feature counts. This gives a breakdown of what happened to reads that were not assigned. Y…
Comment: Incosistencies in buildSNNGraph() function by ATpoint ★ 5.0k
Just played with this a bit and I think it comes down to not having a fixed seed before running the leiden thingy. Same goes for PCA and UM…
Answer: Incosistencies in buildSNNGraph() function by Aaron Lun ★ 29k
The most obvious thing that comes to mind is the RNG seed. `cluster_leiden()` does some random number generation, somewhere deep in the **i…
Comment: Opportunity to host EuroBioC2026 Preconference workshops! by TikTsokaas33ocissalpc • 0
Thank you for sharing the EuroBioC2026 workshop opportunity. I m interested in hosting a hands on session teaching reproducible data analys…
Votes
Answer: Clarification on counting in Rsubread (featureCounts)
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
C: RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
A: Conversion from counts to FPKM
Answer: Incosistencies in buildSNNGraph() function
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