Showing : RNAseq • reset
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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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2
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1.0k
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 18 months ago by ▴ 10 • written 18 months ago by • 0
0
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6
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2.2k
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
18 months ago atan • 0
3
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2
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1.2k
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
18 months ago mohammedtoufiq91 ▴ 10
0
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0
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646
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
18 months ago Bibi • 0
10
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11
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3.2k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 18 months ago by • 0 • written 8.3 years ago by ▴ 80
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3
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1.1k
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 18 months ago by 53k • written 18 months ago by • 0
0
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3
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1.4k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
0
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1
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849
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 19 months ago by 43k • written 19 months ago by • 0
0
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2
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797
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 19 months ago by • 0
0
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2
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1.2k
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
19 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 18 months ago by 53k • written 19 months ago by • 0
0
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1
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1.3k
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 19 months ago by 43k • written 19 months ago by • 0
0
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1
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989
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
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2
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2.0k
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
20 months ago kcarey • 0
2
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2
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848
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
20 months ago Sabiha ▴ 20
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2
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3.0k
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
20 months ago kcarey • 0
1
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4
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909
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DESeq2 Replicates
DESeq2 RNASeq
20 months ago kcarey • 0
1
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3
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1.1k
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 21 months ago by ★ 1.4k • written 21 months ago by ▴ 10
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4
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1.0k
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
21 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 21 months ago by 53k • written 21 months ago by • 0
3
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5
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1.7k
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
2
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1
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742
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
3
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7
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1.9k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
21 months ago • updated 10 weeks ago boczniak767 ▴ 740
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0
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763
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
21 months ago Abril • 0
2
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2
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1.7k
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
21 months ago jackafiore • 0
1
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2
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2.4k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.6 years ago by • 0
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4
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1.0k
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Ballgown error in scan for c.tab files
ballgown RNASeq
22 months ago candacenewcome • 0
1
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3
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1.2k
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
22 months ago island • 0
1
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3
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1.3k
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 22 months ago by • 0
0
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1
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663
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 22 months ago by ▴ 220 • written 22 months ago by • 0
2
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4
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2.2k
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
22 months ago Sabiha ▴ 20
4
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6
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1.7k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 21 months ago by 53k • written 22 months ago by • 0
3
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1
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903
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 22 months ago by 53k • written 22 months ago by • 0
0
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3
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1.5k
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dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 22 months ago by • 0
0
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1
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808
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
22 months ago WS • 0
2
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3
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3.6k
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Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 23 months ago by ★ 1.4k • written 23 months ago by • 0
1
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2
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1.3k
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
23 months ago Sabiha ▴ 20
1
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2
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1.2k
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
24 months ago drewhaydensteele • 0
12
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5
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5.1k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by • 0 • written 24 months ago by • 0
0
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3
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1.3k
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
2.0 years ago • updated 24 months ago Karthik • 0
1
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1
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768
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Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 24 months ago by 43k • written 2.0 years ago by • 0
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3
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1.5k
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
2.0 years ago • updated 24 months 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
2.0 years ago Manthos • 0
2
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4
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1.4k
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limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
2.0 years ago Tyler Sagendorf ▴ 10
0
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1
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817
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DESeq2 model for two genome system
RNASeq DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
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2
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1.3k
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TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 2.1 years ago by ★ 1.1k • written 2.1 years ago by ▴ 200
0
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9
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3.2k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 2.1 years ago by • 0 • written 8.1 years ago by ▴ 60
1
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4
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1.5k
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.1 years ago Wending • 0
0
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0
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835
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
2.1 years ago mch • 0
1,410 results • Page 2 of 29
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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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