Showing : RNASEQ • reset
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 1 day ago by 41k • written 2 days ago by • 0
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1
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98
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 3 days ago by 50k • written 3 days ago by • 0
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2
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159
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
7 days ago • updated 4 days ago catv • 0
3
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1
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122
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Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 8 days ago by • 0
0
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1
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90
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 8 days ago by 41k • written 8 days ago by • 0
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1
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122
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 16 days ago by ★ 4.0k • written 18 days ago by • 0
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2
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213
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
5 weeks ago kcarey • 0
2
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2
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248
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
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2
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246
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
6 weeks ago kcarey • 0
1
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4
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294
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DESeq2 Replicates
DESeq2 RNASeq
7 weeks ago kcarey • 0
1
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3
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345
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 7 weeks ago by ★ 1.3k • written 7 weeks ago by ▴ 10
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4
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277
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 weeks ago mperalc • 0
0
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2
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269
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Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
3
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5
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605
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 8 weeks ago by ▴ 10
2
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1
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247
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
3
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6
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509
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Average biological replicates in RNA-seq
Mfuzz RNASeq
9 weeks ago boczniak767 ▴ 720
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209
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
10 weeks ago Abril • 0
2
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2
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386
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
11 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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377
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Ballgown error in scan for c.tab files
ballgown RNASeq
12 weeks ago candacenewcome • 0
1
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3
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322
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DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
12 weeks ago island • 0
1
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3
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555
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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
222
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 190 • written 3 months ago by • 0
2
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4
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552
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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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560
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
3
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1
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271
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
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3
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461
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dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
0
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1
reply
257
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
2
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3
replies
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 4 months ago by ★ 1.3k • written 4 months ago by • 0
1
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2
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438
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
1
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2
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423
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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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773
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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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442
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago • updated 4 months ago Karthik • 0
1
vote
1
reply
368
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Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 5 months ago by 41k • written 5 months ago by • 0
2
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3
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455
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
2
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2
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392
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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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592
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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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428
views
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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524
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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 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 5 months ago by • 0 • written 6.5 years ago by ▴ 60
1
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4
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611
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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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344
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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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596
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 5 months ago by 50k • written 6 months ago by ▴ 10
0
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6
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815
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
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0
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329
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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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625
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Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
6 months ago Karthik • 0
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0
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267
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
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0
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327
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Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
6 months ago Xinqi • 0
0
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0
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335
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
6 months ago Sara • 0
1
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1
reply
404
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 6 months ago by 65k • written 6 months ago by • 0
50 results • Page 1 of 1
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Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
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