Showing : Rnaseq • reset
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How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 5 hours ago by 65k • written 13 hours ago by • 0
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31
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
1 day ago Bibi • 0
10
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10
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1.9k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 4 days ago by ▴ 220 • written 6.7 years ago by ▴ 80
1
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3
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256
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 5 days ago by 50k • written 6 days ago by • 0
0
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3
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228
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 18 days ago by ★ 4.1k • written 18 days ago by • 0
0
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1
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166
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 25 days ago by 42k • written 26 days ago by • 0
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2
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192
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 27 days ago by • 0
0
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2
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245
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
4 weeks ago • updated 28 days ago catv • 0
5
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3
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319
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Log-cpm values from limma
limma edgeR RNASeq
updated 10 days ago by 50k • written 4 weeks ago by • 0
0
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1
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129
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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1
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155
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 5 weeks ago by ★ 4.1k • written 6 weeks ago by • 0
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2
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272
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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
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2
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320
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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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335
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DESeq2 Replicates
DESeq2 RNASeq
10 weeks ago kcarey • 0
1
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3
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391
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DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 11 weeks ago by ★ 1.4k • written 11 weeks ago by ▴ 10
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4
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328
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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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348
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
3
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5
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673
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 11 weeks ago by 42k • written 12 weeks ago by ▴ 10
2
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1
reply
281
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 12 weeks ago by 42k • written 12 weeks ago by ▴ 10
3
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6
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594
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
3 months ago • updated 12 weeks ago boczniak767 ▴ 720
0
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0
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243
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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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441
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Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
1
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2
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1.2k
views
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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444
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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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361
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
3
replies
630
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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
votes
1
reply
261
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 210 • written 3 months ago by • 0
2
votes
4
replies
653
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago • updated 3 months ago Sabiha ▴ 20
4
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6
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653
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
3
votes
1
reply
331
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
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3
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554
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dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 4 months ago by • 0
0
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1
reply
290
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DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
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 5 months ago by ★ 1.4k • written 5 months ago by • 0
1
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2
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498
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago Sabiha ▴ 20
1
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2
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472
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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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866
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
votes
3
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485
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
6 months ago • updated 5 months ago Karthik • 0
1
vote
1
reply
395
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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526
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
2
votes
2
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440
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
6 months ago Manthos • 0
2
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4
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646
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
6 months ago Tyler Sagendorf ▴ 10
0
votes
1
reply
462
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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2
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565
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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9
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2.5k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 6 months ago by • 0 • written 6.6 years ago by ▴ 60
1
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4
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665
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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375
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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684
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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924
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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353
views
is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
7 months ago Sara • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Help with ENmix readidat by James W. MacDonald 65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Comment: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
We have some text about this particular question in the Frequently Asked Questions (FAQ) part of the software vignette.
Votes
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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