Showing : RnaSeq • reset
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
deconvolution rnaseqGene RNAseq
19 months ago JG13 • 0
0
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1
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772
views
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
1
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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
20 months ago • updated 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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0
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681
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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
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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
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3
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1.6k
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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
0
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1
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900
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 21 months ago by 43k • written 21 months ago by • 0
0
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2
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839
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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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1.7k
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Log-cpm values from limma
limma edgeR RNASeq
updated 20 months ago by 53k • written 21 months ago by • 0
0
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1
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1.5k
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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
views
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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2.2k
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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907
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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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3.6k
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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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960
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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
23 months ago • updated 22 months ago mperalc • 0
0
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2
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1.2k
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 23 months ago by 53k • written 23 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 23 months ago by ▴ 10
2
votes
1
reply
791
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 23 months ago by 43k • written 23 months ago by ▴ 10
3
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7
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2.0k
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
23 months ago • updated 4 months ago boczniak767 ▴ 740
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0
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799
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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
24 months ago • updated 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 24 months ago by • 0
0
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1
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697
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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2.6k
views
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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1.8k
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
reply
946
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
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 2.0 years ago by • 0
0
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1
reply
865
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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3.9k
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
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2
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1.3k
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
replies
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
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
2.2 years ago • updated 2.1 years ago Karthik • 0
1
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1
reply
810
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 2.1 years ago by 43k • written 2.2 years ago by • 0
2
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3
replies
1.6k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
2.2 years ago • updated 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
2.2 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
reply
868
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
views
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
1,412 results • Page 2 of 29
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Comment: Pairwise comparison of multiple groups with different base by ja569116 • 0
Hi @mikelove I have a similar situation, and I feel that I have interpreted the results in the wrong way. In my case I would like to identi…
Comment: Are individual-mouse-based statistics possible in CellChat? by TikTsossakaas33ocissalpc • 0
Questions about comparing groups and statistical significance highlight how data driven thinking matters across fields. In online mobile ga…
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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