Showing : RNAseq • reset
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 3 days ago by 50k • written 4 days ago by • 0
0
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3
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221
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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 16 days ago by • 0
0
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1
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165
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 23 days ago by 42k • written 23 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 25 days ago by • 0
0
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2
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237
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
28 days ago • updated 26 days ago catv • 0
0
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1
reply
125
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 29 days ago by 42k • written 4 weeks ago by • 0
5
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3
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304
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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
154
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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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266
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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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329
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DESeq2 Replicates
DESeq2 RNASeq
10 weeks ago kcarey • 0
1
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3
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386
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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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323
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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
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Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
2
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1
reply
278
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 11 weeks ago by 42k • written 11 weeks ago by ▴ 10
3
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5
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668
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 10 weeks ago by 42k • written 12 weeks ago by ▴ 10
3
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6
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585
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Average biological replicates in RNA-seq
Mfuzz RNASeq
12 weeks ago boczniak767 ▴ 720
0
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0
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242
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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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437
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
0
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4
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440
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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
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
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3
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622
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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
reply
256
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 210 • written 3 months ago by • 0
2
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4
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648
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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640
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
3
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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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544
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 4 months ago by • 0
0
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1
reply
287
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
1
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2
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493
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
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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468
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
7
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2
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862
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
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
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3
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519
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
0
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3
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480
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
2
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2
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438
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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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641
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
1
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4
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658
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
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374
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
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2
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674
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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919
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
0
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2
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563
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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1
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460
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 6 months ago by 42k • written 7 months ago by • 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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661
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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299
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
7 months ago Florian • 0
0
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0
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357
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
7 months ago Xinqi • 0
0
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0
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381
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
7 months ago Sara • 0
1
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1
reply
444
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 7 months ago by 65k • written 7 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
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…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
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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