Showing : RNASeq • reset
10
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10
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1.9k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 2 days ago by ▴ 220 • written 6.7 years ago by ▴ 80
1
vote
3
replies
238
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 days ago by 50k • written 5 days ago by • 0
0
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3
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223
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
0
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1
reply
165
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 24 days ago by 42k • written 24 days ago by • 0
0
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2
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190
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 26 days ago by • 0
0
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2
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239
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
29 days ago • updated 26 days ago catv • 0
5
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3
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307
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Log-cpm values from limma
limma edgeR RNASeq
updated 8 days ago by 50k • written 4 weeks ago by • 0
0
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1
reply
128
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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1
reply
154
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
0
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2
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267
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
8 weeks ago kcarey • 0
2
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2
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289
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
0
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2
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313
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
9 weeks ago kcarey • 0
1
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4
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330
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DESeq2 Replicates
DESeq2 RNASeq
10 weeks ago kcarey • 0
1
vote
3
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388
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 10 weeks ago by ★ 1.4k • written 11 weeks ago by ▴ 10
0
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4
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325
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
0
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2
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345
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
3
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5
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670
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 12 weeks ago by ▴ 10
2
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1
reply
279
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by ▴ 10
3
votes
6
replies
587
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
12 weeks ago boczniak767 ▴ 720
0
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0
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242
views
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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438
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
1
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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
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4
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440
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
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3
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359
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
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3
replies
624
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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
votes
1
reply
259
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 210 • written 3 months ago by • 0
2
votes
4
replies
648
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
4
votes
6
replies
641
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
327
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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546
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 4 months ago by • 0
0
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1
reply
288
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
2
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3
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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 4 months ago by ★ 1.4k • written 5 months ago by • 0
1
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2
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493
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago • updated 4 months ago Sabiha ▴ 20
1
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2
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468
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
7
votes
2
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864
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
481
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
1
vote
1
reply
394
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 5 months ago by 42k • written 5 months ago by • 0
2
votes
3
replies
522
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
2
votes
2
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438
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 • updated 5 months ago Manthos • 0
2
votes
4
replies
644
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
462
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
564
views
TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 6 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 6 months ago by • 0 • written 6.6 years ago by ▴ 60
1
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4
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661
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
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0
replies
375
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
675
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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920
views
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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352
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
7 months ago Sara • 0
0
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2
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662
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
7 months ago • updated 6 months ago Karthik • 0
0
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0
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300
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
7 months ago Florian • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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