Showing : RNASeq • reset
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
4 hours ago james.zhang20 • 0
8
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6
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1.7k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 1 day ago by ▴ 200 • written 6.7 years ago by ▴ 80
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1
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124
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 7 days ago by 41k • written 7 days ago by • 0
0
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1
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130
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
updated 9 days ago by 50k • written 9 days ago by • 0
0
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2
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192
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
12 days ago • updated 9 days ago catv • 0
3
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1
reply
156
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Log-cpm values from limma
limma edgeR RNASeq
updated 12 days ago by 50k • written 13 days ago by • 0
0
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1
reply
100
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 13 days ago by 41k • written 13 days ago by • 0
0
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1
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133
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 21 days ago by ★ 4.1k • written 23 days ago by • 0
0
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2
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225
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 weeks ago • updated 5 weeks ago kcarey • 0
2
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2
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255
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
0
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2
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258
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RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 weeks ago • updated 6 weeks ago kcarey • 0
1
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4
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301
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DESeq2 Replicates
DESeq2 RNASeq
8 weeks ago kcarey • 0
1
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3
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355
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 8 weeks ago by ★ 1.3k • written 8 weeks ago by ▴ 10
0
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4
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293
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago • updated 8 weeks ago mperalc • 0
0
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2
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288
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Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
3
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5
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615
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DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 8 weeks ago by 41k • written 9 weeks ago by ▴ 10
2
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1
reply
258
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 9 weeks ago by 41k • written 9 weeks ago by ▴ 10
3
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6
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522
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Average biological replicates in RNA-seq
Mfuzz RNASeq
10 weeks ago boczniak767 ▴ 720
0
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0
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218
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 weeks ago Abril • 0
2
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2
replies
401
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
12 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 12 months ago by • 0
0
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4
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390
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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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332
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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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565
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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
230
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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577
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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
votes
6
replies
580
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 12 weeks ago by 50k • written 3 months ago by • 0
3
votes
1
reply
289
views
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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475
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
0
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1
reply
265
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
3 months ago WS • 0
2
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3
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1.2k
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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451
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
1
vote
2
replies
437
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago • updated 4 months ago drewhaydensteele • 0
7
votes
2
replies
792
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
0
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3
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452
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
1
vote
1
reply
373
views
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
votes
3
replies
467
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
2
votes
2
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401
views
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
votes
4
replies
601
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
433
views
DESeq2 model for two genome system
RNASeq DESeq2
updated 5 months ago by 41k • written 6 months ago by • 0
0
votes
2
replies
530
views
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
replies
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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621
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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351
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
votes
2
replies
619
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
replies
839
views
DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 months ago erika.maldonado-rosado • 0
0
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0
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334
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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635
views
Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
6 months ago Karthik • 0
0
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0
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276
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
0
votes
0
replies
334
views
Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
6 months ago Xinqi • 0
50 results • Page 1 of 1
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
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Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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