Showing : rnaseq • reset
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102
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 7 days ago by ★ 4.0k • written 9 days ago by • 0
0
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2
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191
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
28 days ago • updated 27 days ago kcarey • 0
2
votes
2
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233
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
4 weeks ago Sabiha ▴ 20
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2
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223
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 weeks ago • updated 4 weeks ago kcarey • 0
1
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4
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279
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DESeq2 Replicates
DESeq2 RNASeq
6 weeks ago kcarey • 0
1
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3
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324
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 6 weeks ago by ★ 1.3k • written 6 weeks ago by ▴ 10
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4
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260
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
7 weeks ago • updated 6 weeks ago mperalc • 0
0
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2
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247
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Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
3
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5
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583
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 weeks ago by 41k • written 7 weeks ago by ▴ 10
2
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1
reply
234
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 7 weeks ago by 41k • written 7 weeks ago by ▴ 10
3
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6
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484
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Average biological replicates in RNA-seq
Mfuzz RNASeq
8 weeks ago boczniak767 ▴ 720
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0
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186
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 weeks ago Abril • 0
2
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2
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354
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
10 weeks ago jackafiore • 0
1
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2
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1.1k
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How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
0
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4
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355
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Ballgown error in scan for c.tab files
ballgown RNASeq
11 weeks ago • updated 10 weeks ago candacenewcome • 0
1
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3
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312
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
11 weeks ago island • 0
1
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3
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539
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 11 weeks ago by • 0
0
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1
reply
213
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 12 weeks ago by ▴ 190 • written 12 weeks ago by • 0
2
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4
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516
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
12 weeks ago Sabiha ▴ 20
4
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6
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537
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 weeks ago by 50k • written 3 months ago by • 0
3
votes
1
reply
245
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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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430
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dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
0
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1
reply
245
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
2
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3
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1.1k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 3 months ago by ★ 1.3k • written 4 months ago by • 0
1
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2
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415
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
3 months ago Sabiha ▴ 20
1
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2
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408
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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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712
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
3
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427
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
4 months ago Karthik • 0
1
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1
reply
360
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 4 months ago by 41k • written 4 months ago by • 0
2
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3
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437
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
4 months ago Karthik • 0
2
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2
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383
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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
4 months ago Manthos • 0
2
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4
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578
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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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414
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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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507
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TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 5 months ago by ★ 1.0k • written 5 months ago by ▴ 190
0
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9
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2.4k
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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589
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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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333
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
5 months ago mch • 0
4
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2
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568
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 5 months ago by 50k • written 5 months ago by ▴ 10
0
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6
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788
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
5 months ago erika.maldonado-rosado • 0
0
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0
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316
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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616
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
6 months ago • updated 5 months ago Karthik • 0
0
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0
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255
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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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316
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
6 months ago Xinqi • 0
0
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0
replies
314
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
6 months ago Sara • 0
1
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1
reply
391
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
1
vote
7
replies
791
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 4 months ago by 50k • written 6 months ago by • 0
0
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2
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399
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 6 months ago by ★ 1.3k • written 6 months ago by • 0
0
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1
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384
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 6 months ago by ▴ 760 • written 6 months ago by • 0
3
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5
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792
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
1
vote
1
reply
431
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
50 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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