0
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3
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249
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A ComBat-seq issue: the covariates are confounded
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updated 13 days ago by ▴ 850 • written 20 days ago by • 0
0
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
20 days ago Stevie Pederson • 0
2
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2
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379
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
20 days ago • updated 19 days ago Henry ▴ 10
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News: Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
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21 days ago communication • 0
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382
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Memory errors using read.bismark?
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3
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6
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264
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Surrogate variable analysis for paired RNA seq experiment
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21 days ago • updated 20 days ago nhaus ▴ 30
0
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136
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The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 16 days ago by • 0 • written 21 days ago by • 0
0
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173
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DESeq2 gives an error and R crashes
DESeq2
21 days ago • updated 20 days ago Shefali • 0
1
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2
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237
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How to retrieve detailed regression results from deseq2
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21 days ago • updated 12 days ago Weiqian ▴ 10
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Light difference when using coef vs omit a group when compare 3 groups.
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21 days ago • updated 14 days ago Chris • 0
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126
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LearnTaxa with custom Silva
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21 days ago Eryn • 0
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queryDGIdb lexical error for some genes
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21 days ago Dennis • 0
0
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1
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154
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compareCluster dotplot: how to modify the genesets order
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updated 18 days ago by ★ 3.9k • written 21 days ago by • 0
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4
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Storing directories inside an ExperimentHub package?
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21 days ago • updated 20 days ago Tim Barry • 0
8
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23
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912
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Convert Seurat Object to Summarised Experiment or ExpressionSet
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updated 20 days ago by ★ 3.3k • written 21 days ago by ▴ 40
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342
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Why is my gene not significantly differentially expressed?
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updated 17 days ago by 50k • written 22 days ago by • 0
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146
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BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 22 days ago by 65k • written 22 days ago by • 0
0
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1
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157
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 22 days ago by 41k • written 22 days ago by • 0
5
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6
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414
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
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0
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106
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ggtree tip label position (depth)
ggtree
23 days ago • updated 22 days ago Roope • 0
1
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6
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479
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GSVA on separate healthy and disease datasets
GSVA
updated 22 days ago by 65k • written 23 days ago by ▴ 60
2
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How to make boxplot with pairwise and overall p value from Limma
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23 days ago Chris • 0
0
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Can you find the correct transcript in scRNA seq data
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updated 22 days ago by ★ 4.1k • written 24 days ago by • 0
0
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Job: PhD-position in bioinformatics / computational biology
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24 days ago arne.sahm • 0
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94
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News: Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
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24 days ago Wolfgang Huber ★ 13k
3
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3
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permutation test in edgeR
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updated 11 days ago by 50k • written 24 days ago by • 0
0
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176
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How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
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updated 23 days ago by 65k • written 24 days ago by • 0
0
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157
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
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4
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limma
26 days ago • updated 25 days ago andrea.rodriguez-martinez13 • 0
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3
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edgeR DifferentialExpression
updated 26 days ago by 65k • written 26 days ago by • 0
0
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0
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Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
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26 days ago andromeda • 0
0
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2
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159
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What to the log 2 fold changes mean using LRT on time course in DESeq2
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updated 27 days ago by 65k • written 27 days ago by • 0
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2
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214
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updated 22 days ago by 41k • written 27 days ago by ▴ 30
2
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2
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183
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Bluster and Varieties of Louvain Clulstering
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updated 27 days ago by ★ 4.1k • written 27 days ago by ★ 1.5k
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1
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126
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Granges regionCounts not returning the expected number of entries
methylKit
27 days ago • updated 26 days ago Modoc Kesner ▴ 10
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flowDensity on a flowset
flowDensity
27 days ago fredrikwallberg • 0
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2
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233
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Regressing out batch effects
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updated 22 days ago by 41k • written 27 days ago by • 0
1
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1
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160
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DESeq2 - Missing values in count matrix
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updated 27 days ago by 65k • written 28 days ago by • 0
0
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DMRcate error need at least two non-NA values to interpolate
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28 days ago Macsue • 0
0
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1
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232
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CombineArrays for EPIC and EPIC V2
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updated 28 days ago by ▴ 170 • written 28 days ago by • 0
1
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6
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419
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 28 days ago by 41k • written 28 days ago by • 0
1
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4
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427
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Using a change in a continuous explanatory variable to test changes in gene expression with limma
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updated 27 days ago by 50k • written 29 days ago by • 0
0
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2
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
29 days ago Marianna ▴ 20
0
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2
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183
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voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
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29 days ago • updated 28 days ago Gimena • 0
0
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6
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323
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unable to access Annotationhub latest record
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updated 21 days ago by ▴ 170 • written 29 days ago by • 0
1
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10
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438
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Obtaining pheno data from CEL files
GEO affy
29 days ago • updated 23 days ago Kurtis • 0
1
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1
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148
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago • updated 29 days ago Layal • 0
0
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2
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166
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pca with VST of DESeq2 give 100% variance in PC1
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4 weeks ago • updated 29 days ago michelafrancesconi8 • 0
0
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1
reply
138
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Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
0
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4
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251
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Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 29 days ago by 41k • written 4 weeks ago by • 0
45,603 results • Page 3 of 913
Recent ...
Replies
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Answer: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
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A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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