0
votes
3
replies
204
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 18 days ago by 41k • written 19 days ago by ▴ 20
2
votes
3
replies
324
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
20 days ago • updated 19 days ago daniel.carbajo • 0
0
votes
4
replies
265
views
DEG with low counts
DESeq2
updated 15 days ago by 41k • written 20 days ago by • 0
1
vote
2
replies
511
views
GSVA error
GSVA
20 days ago • updated 19 days ago Alex • 0
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 19 days ago by ★ 4.1k • written 21 days ago by • 0
1
vote
1
reply
185
views
Differentially expressed genes in monocle pseudotime
monocle
updated 18 days ago by 50k • written 21 days ago by • 0
0
votes
1
reply
138
views
SNP locus package for mouse?
SNPlocs packFinder
updated 18 days ago by 65k • written 21 days ago by • 0
2
votes
2
replies
171
views
[DiffBind] Obtaining normalization factors
DiffBind
22 days ago • updated 18 days ago Henry ▴ 10
1
vote
2
replies
193
views
Design Matrix within group comparison more than two groups
DESeq2
22 days ago • updated 21 days ago hemantcnaik • 0
0
votes
1
reply
132
views
Bioinformatics student
Des DESeq2
updated 22 days ago by • 0 • written 22 days ago by • 0
2
votes
2
replies
191
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
22 days ago julia_mcdonough • 0
0
votes
0
replies
84
views
News: Important Release 3.18 Freeze Announcment
Release release Bioconductor Bioconducto
22 days ago shepherl 3.9k
3
votes
3
replies
201
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
22 days ago • updated 16 days ago jacques.imbert • 0
2
votes
2
replies
171
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
22 days ago • updated 20 days ago daniel.carbajo • 0
0
votes
3
replies
254
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 16 days ago by ▴ 850 • written 22 days ago by • 0
0
votes
0
replies
91
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
23 days ago Stevie Pederson • 0
2
votes
2
replies
386
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
23 days ago • updated 22 days ago Henry ▴ 10
0
votes
0
replies
99
views
News: Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing Sequencing SequencingData
23 days ago communication • 0
4
votes
8
replies
391
views
Memory errors using read.bismark?
dmrseq bsseq
updated 16 days ago by ▴ 740 • written 23 days ago by • 0
3
votes
6
replies
270
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
23 days ago nhaus ▴ 30
0
votes
1
reply
142
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 19 days ago by • 0 • written 23 days ago by • 0
0
votes
1
reply
174
views
DESeq2 gives an error and R crashes
DESeq2
24 days ago • updated 23 days ago Shefali • 0
1
vote
2
replies
241
views
How to retrieve detailed regression results from deseq2
DESeq2
24 days ago • updated 15 days ago Weiqian ▴ 10
5
votes
9
replies
923
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
24 days ago • updated 16 days ago Chris • 0
0
votes
0
replies
130
views
LearnTaxa with custom Silva
DECIPHER LearnTaxa
24 days ago Eryn • 0
0
votes
0
replies
85
views
queryDGIdb lexical error for some genes
lexicalerror rDGIdb DGIdb json
24 days ago Dennis • 0
0
votes
1
reply
158
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 20 days ago by ★ 3.9k • written 24 days ago by • 0
0
votes
4
replies
222
views
Storing directories inside an ExperimentHub package?
ExperimentHub
24 days ago • updated 23 days ago Tim Barry • 0
8
votes
23
replies
936
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 23 days ago by ★ 3.3k • written 24 days ago by ▴ 40
1
vote
3
replies
347
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 19 days ago by 50k • written 25 days ago by • 0
0
votes
1
reply
149
views
BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 25 days ago by 65k • written 25 days ago by • 0
0
votes
1
reply
161
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 25 days ago by 41k • written 25 days ago by • 0
5
votes
6
replies
425
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 22 days ago by ★ 4.1k • written 25 days ago by ▴ 30
0
votes
0
replies
111
views
ggtree tip label position (depth)
ggtree
25 days ago • updated 24 days ago Roope • 0
1
vote
6
replies
490
views
GSVA on separate healthy and disease datasets
GSVA
updated 24 days ago by 65k • written 25 days ago by ▴ 60
2
votes
6
replies
398
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
26 days ago Chris • 0
0
votes
1
reply
139
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 24 days ago by ★ 4.1k • written 26 days ago by • 0
0
votes
0
replies
144
views
Job: PhD-position in bioinformatics / computational biology
Mergeomics Epigenome Evolution NGS Aging
26 days ago arne.sahm • 0
0
votes
0
replies
96
views
News: Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry conference
26 days ago Wolfgang Huber ★ 13k
3
votes
3
replies
333
views
permutation test in edgeR
rna-seq edgeR
updated 14 days ago by 50k • written 27 days ago by • 0
0
votes
1
reply
180
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 26 days ago by 65k • written 27 days ago by • 0
0
votes
1
reply
164
views
Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 28 days ago by 50k • written 29 days ago by • 0
0
votes
4
replies
307
views
Help with design.matrix
limma
29 days ago • updated 28 days ago andrea.rodriguez-martinez13 • 0
1
vote
3
replies
253
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 29 days ago by 65k • written 29 days ago by • 0
0
votes
0
replies
143
views
Why output of GSEA is not the same but inversed, when you have the same but inversed input data?
clusterProfiler gseKEGG
29 days ago andromeda • 0
0
votes
2
replies
167
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 29 days ago by 65k • written 29 days ago by • 0
0
votes
2
replies
219
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 25 days ago by 41k • written 29 days ago by ▴ 30
2
votes
2
replies
194
views
Bluster and Varieties of Louvain Clulstering
bluster
updated 29 days ago by ★ 4.1k • written 4 weeks ago by ★ 1.5k
0
votes
1
reply
130
views
Granges regionCounts not returning the expected number of entries
methylKit
4 weeks ago • updated 29 days ago Modoc Kesner ▴ 10
0
votes
0
replies
103
views
flowDensity on a flowset
flowDensity
4 weeks ago fredrikwallberg • 0
1,000 results • Page 3 of 20
Recent ...
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
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Comment: Too many significant genes when integrating gtex and tcga
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