Showing : rnaseq • reset
0
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
updated 2 days ago by ★ 3.6k • written 3 days ago by • 0
2
votes
2
replies
140
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Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
5 days ago • updated 4 days ago mohammedtoufiq91 ▴ 10
1
vote
1
reply
195
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 6 days ago by 66k • written 6 days ago by • 0
0
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0
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52
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
7 days ago Bibi • 0
10
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11
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1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 4 days ago by • 0 • written 6.8 years ago by ▴ 80
1
vote
3
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288
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 12 days ago by 50k • written 13 days ago by • 0
0
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3
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247
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 24 days ago by ★ 4.2k • written 25 days ago by • 0
0
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1
reply
176
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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2
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202
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 4 weeks ago by • 0
0
votes
2
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255
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 weeks ago • updated 4 weeks ago catv • 0
5
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3
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333
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Log-cpm values from limma
limma edgeR RNASeq
updated 16 days ago by 50k • written 5 weeks ago by • 0
0
votes
1
reply
138
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
votes
1
reply
160
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
0
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2
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290
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
9 weeks ago kcarey • 0
2
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2
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295
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 weeks ago Sabiha ▴ 20
0
votes
2
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337
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
10 weeks ago kcarey • 0
1
vote
4
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343
views
DESeq2 Replicates
DESeq2 RNASeq
11 weeks ago kcarey • 0
1
vote
3
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400
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 11 weeks ago by ★ 1.4k • written 12 weeks ago by ▴ 10
0
votes
4
replies
340
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
12 weeks ago mperalc • 0
0
votes
2
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362
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 3 months ago by 50k • written 3 months ago by • 0
3
votes
5
replies
680
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 11 weeks ago by 42k • written 3 months ago by ▴ 10
2
votes
1
reply
282
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 3 months ago by 42k • written 3 months ago by ▴ 10
3
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6
replies
613
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
3 months ago boczniak767 ▴ 720
0
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0
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251
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
3 months ago Abril • 0
2
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2
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453
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
1
vote
2
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1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
4
replies
450
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
vote
3
replies
368
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
3
replies
643
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 4 months ago by • 0
0
votes
1
reply
269
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 4 months ago by ▴ 210 • written 4 months ago by • 0
2
votes
4
replies
670
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
4
votes
6
replies
660
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
3
votes
1
reply
340
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
0
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3
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579
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 4 months ago by • 0
0
votes
1
reply
294
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
1
vote
2
replies
508
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago Sabiha ▴ 20
1
vote
2
replies
477
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
7
votes
2
replies
896
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
votes
3
replies
499
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
6 months ago • updated 5 months ago Karthik • 0
1
vote
1
reply
398
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 6 months ago by 42k • written 6 months ago by • 0
2
votes
3
replies
539
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
6 months ago Karthik • 0
2
votes
2
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444
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
6 months ago Manthos • 0
2
votes
4
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654
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
464
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 6 months ago by 42k • written 7 months ago by • 0
0
votes
2
replies
570
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 6 months ago by ★ 1.1k • written 7 months ago by ▴ 190
0
votes
9
replies
2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 6 months ago by • 0 • written 6.6 years ago by ▴ 60
1
vote
4
replies
669
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
6 months ago Wending • 0
0
votes
0
replies
378
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
697
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 7 months ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by BioinfGuru ▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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