Showing : RnaSeq • reset
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 5 days ago by 41k • written 5 days ago by • 0
0
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1
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119
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 7 days ago by 50k • written 7 days ago by • 0
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2
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181
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
10 days ago • updated 8 days ago catv • 0
3
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1
reply
150
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Log-cpm values from limma
limma edgeR RNASeq
updated 11 days ago by 50k • written 12 days ago by • 0
0
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1
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96
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 11 days ago by 41k • written 12 days ago by • 0
0
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1
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127
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 20 days ago by ★ 4.1k • written 21 days ago by • 0
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2
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218
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago kcarey • 0
2
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2
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251
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
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2
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254
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago kcarey • 0
1
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4
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298
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DESeq2 Replicates
DESeq2 RNASeq
7 weeks ago kcarey • 0
1
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3
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351
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 weeks ago by ★ 1.3k • written 8 weeks ago by ▴ 10
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4
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287
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 weeks ago mperalc • 0
0
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2
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279
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
3
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5
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610
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 9 weeks ago by ▴ 10
2
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1
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250
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 weeks ago by 41k • written 9 weeks ago by ▴ 10
3
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6
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519
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Average biological replicates in RNA-seq
Mfuzz RNASeq
10 weeks ago • updated 9 weeks ago boczniak767 ▴ 720
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211
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
10 weeks ago Abril • 0
2
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2
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394
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
11 weeks ago jackafiore • 0
1
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2
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1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
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4
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384
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Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago • updated 12 weeks ago candacenewcome • 0
1
vote
3
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328
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago • updated 12 weeks ago island • 0
1
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3
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562
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
0
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1
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227
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 190 • written 3 months ago by • 0
2
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4
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567
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
4
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6
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570
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
3
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1
reply
280
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
0
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3
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471
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dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
0
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1
reply
261
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
2
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3
replies
1.2k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
1
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2
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445
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
1
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2
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430
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
4 months ago drewhaydensteele • 0
7
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2
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781
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
0
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3
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448
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
1
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1
reply
371
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 5 months ago by 41k • written 5 months ago by • 0
2
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3
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464
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
2
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2
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396
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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
5 months ago Manthos • 0
2
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4
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595
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
0
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1
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431
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 5 months ago by 41k • written 6 months ago by • 0
0
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2
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528
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 5 months ago by ★ 1.0k • written 6 months ago by ▴ 190
0
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9
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2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 5 months ago by • 0 • written 6.5 years ago by ▴ 60
1
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4
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616
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
5 months ago Wending • 0
0
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0
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349
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
6 months ago mch • 0
4
votes
2
replies
608
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
0
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6
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827
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
0
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0
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332
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
6 months ago Sara • 0
0
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2
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630
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
6 months ago Karthik • 0
0
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0
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272
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
0
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0
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331
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
6 months ago Xinqi • 0
0
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0
replies
341
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
6 months ago Sara • 0
1
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1
reply
411
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
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Comment: Fold change calculation in Diffbind vs. DESEQ2? by Pepko • 0
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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Thanks Gordon for a detail guide! Seem you track time of everything.
Answer: Version 3.15 S4Vectors packages are missing by shepherl 3.8k
It is missing because that package did not have any updates in the release except for the initial version. The archive directory holds prev…
Comment: putting my own expression data in deseq2 by ATpoint ★ 4.1k
> directly from GEOquery I can tell you that GEOquery retrieves array data not appropriate for DESeq2. For anything else make your questi…
Comment: Assist me in determining whether the analysis process using the limma package ha by SSSJec • 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
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Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
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Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
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