Showing : RnaSeq • reset
8
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7
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1.7k
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SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 2 days ago by • 0 • written 6.7 years ago by ▴ 80
0
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3
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157
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
0
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2
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172
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limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 15 days ago by • 0
0
votes
1
reply
155
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 13 days ago by 42k • written 14 days ago by • 0
1
vote
3
replies
869
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 14 days ago by ★ 1.2k • written 14 months ago by ▴ 10
0
votes
2
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215
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RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
19 days ago • updated 16 days ago catv • 0
3
votes
1
reply
180
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Log-cpm values from limma
limma edgeR RNASeq
updated 19 days ago by 50k • written 20 days ago by • 0
0
votes
1
reply
113
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 20 days ago by 42k • written 20 days ago by • 0
0
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2
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926
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 21 days ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
142
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 28 days ago by ★ 4.1k • written 4 weeks ago by • 0
0
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5
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1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 5 weeks ago by 50k • written 11.5 years ago by ▴ 30
0
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2
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701
views
biomart not ound some prevous release
biomart rnaseq
written 5.2 years ago by ▴ 40
4
votes
16
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7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 6 weeks ago by • 0 • written 9.0 years ago by ▴ 150
0
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2
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236
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 weeks ago kcarey • 0
0
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5
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9.3k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 7 weeks ago by • 0 • written 7.6 years ago by • 0
0
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2
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280
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
7 weeks ago kcarey • 0
2
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2
replies
266
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Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
0
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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 8 weeks ago by • 0 • written 2.7 years ago by • 0
1
vote
4
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309
views
DESeq2 Replicates
DESeq2 RNASeq
8 weeks ago kcarey • 0
1
vote
3
replies
369
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 9 weeks ago by ★ 1.3k • written 9 weeks ago by ▴ 10
0
votes
3
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496
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
3
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5
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638
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 9 weeks ago by 42k • written 10 weeks ago by ▴ 10
0
votes
4
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305
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 weeks ago • updated 9 weeks ago mperalc • 0
2
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5
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1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
0
votes
2
replies
307
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
2
votes
1
reply
267
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 10 weeks ago by 42k • written 10 weeks ago by ▴ 10
3
votes
6
replies
541
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
11 weeks ago boczniak767 ▴ 720
0
votes
0
replies
226
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 weeks ago Abril • 0
4
votes
6
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607
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 3 months ago by • 0
2
votes
2
replies
415
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
4
replies
403
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
vote
3
replies
340
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
3
replies
589
views
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
240
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 3 months ago by ▴ 210 • written 3 months ago by • 0
2
votes
4
replies
601
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
5
votes
7
replies
10k
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
304
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
5
votes
7
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1.1k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 3 months ago by 50k • written 13 months ago by • 0
0
votes
1
reply
272
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago • updated 3 months ago WS • 0
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 4 months ago by 50k • written 3.0 years ago by ▴ 60
2
votes
3
replies
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
vote
2
replies
473
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
0
votes
2
replies
1.4k
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 15 months ago by • 0
1
vote
8
replies
2.6k
views
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
vote
7
replies
847
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 5 months ago by 50k • written 7 months ago by • 0
1
vote
2
replies
445
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
5 months ago drewhaydensteele • 0
4
votes
4
replies
2.1k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 5 months ago by 50k • written 2.4 years ago by ▴ 10
7
votes
2
replies
813
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
50 results • Page 1 of 1
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Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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