Showing : RNASEQ • reset
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
updated 10 hours ago by 50k • written 18 hours ago by • 0
0
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1
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68
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Log-cpm values from limma
limma edgeR RNASeq
updated 1 day ago by 50k • written 2 days ago by • 0
1
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2
replies
754
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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 1 day ago by • 0 • written 13 months ago by ▴ 10
0
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1
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54
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 1 day ago by 41k • written 2 days ago by • 0
0
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2
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871
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Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 2 days ago by • 0 • written 17 months ago by • 0
0
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1
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107
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 9 days ago by ★ 4.0k • written 11 days ago by • 0
0
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5
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1.8k
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EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 18 days ago by 50k • written 11.5 years ago by ▴ 30
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2
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688
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biomart not ound some prevous release
biomart rnaseq
written 5.2 years ago by ▴ 40
4
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16
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7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 29 days ago by • 0 • written 8.9 years ago by ▴ 150
0
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2
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201
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
4 weeks ago • updated 29 days ago kcarey • 0
0
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5
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9.2k
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tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 4 weeks ago by • 0 • written 7.6 years ago by • 0
0
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2
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227
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
5 weeks ago kcarey • 0
2
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2
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239
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
5 weeks ago Sabiha ▴ 20
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2
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1.3k
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Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 5 weeks ago by • 0 • written 2.6 years ago by • 0
1
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4
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286
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DESeq2 Replicates
DESeq2 RNASeq
6 weeks ago kcarey • 0
1
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3
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333
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 6 weeks ago by ★ 1.3k • written 7 weeks ago by ▴ 10
0
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3
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439
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dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
3
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5
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589
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 6 weeks ago by 41k • written 8 weeks ago by ▴ 10
0
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4
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263
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
7 weeks ago mperalc • 0
2
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5
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1.3k
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edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 13 months ago by • 0
0
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2
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250
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Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
2
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1
reply
238
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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492
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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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192
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 weeks ago Abril • 0
4
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6
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542
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 weeks ago by 50k • written 3 months ago by • 0
2
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2
replies
363
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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
views
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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362
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Ballgown error in scan for c.tab files
ballgown RNASeq
11 weeks ago candacenewcome • 0
1
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3
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315
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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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543
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Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 12 weeks ago by • 0
0
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1
reply
216
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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525
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Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago • updated 12 weeks ago Sabiha ▴ 20
5
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7
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9.9k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
3
votes
1
reply
251
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
5
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7
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1.0k
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different number of DEG because of outliers
DESeq2 RNASeq
updated 3 months ago by 50k • written 13 months ago by • 0
0
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1
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250
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
3
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1
reply
1.6k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 3 months ago by 50k • written 3.0 years ago by ▴ 60
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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421
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
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8
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3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.1 years ago by ▴ 40
0
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2
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1.3k
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 14 months ago by • 0
1
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8
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2.5k
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How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 4 months ago by • 0 • written 3.3 years ago by ▴ 10
1
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7
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799
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
1
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2
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414
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
4 months ago drewhaydensteele • 0
4
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4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.3 years ago by ▴ 10
7
votes
2
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737
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
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3
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432
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
4 months ago Karthik • 0
2
votes
3
replies
443
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
4 months ago Karthik • 0
1
vote
1
reply
362
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
votes
2
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385
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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
50 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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