3
votes
18
replies
2.9k
views
News: List of Deprecated Packages for Bioc3.18
Deprecation devel Bioconductor Devel
10 months ago • updated 16 days ago shepherl 3.9k
0
votes
1
reply
137
views
SNP locus package for mouse?
SNPlocs packFinder
updated 17 days ago by 65k • written 20 days ago by • 0
1
vote
2
replies
133
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
17 days ago Ana • 0
0
votes
5
replies
1.7k
views
blockwiseModule crashes in the end and doesn't generate modules
WGCNA
written 12 months ago by • 0
0
votes
1
reply
119
views
what is the sampleFiles
chipseq
updated 17 days ago by 65k • written 17 days ago by • 0
1
vote
1
reply
182
views
Differentially expressed genes in monocle pseudotime
monocle
updated 17 days ago by 50k • written 19 days ago by • 0
4
votes
8
replies
387
views
Memory errors using read.bismark?
dmrseq bsseq
updated 15 days ago by ▴ 740 • written 22 days ago by • 0
3
votes
3
replies
197
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
21 days ago • updated 15 days ago jacques.imbert • 0
0
votes
1
reply
140
views
The issue with SGSeq_analyzeFeatures() returns errors on BAM files
SGSeq
updated 17 days ago by • 0 • written 22 days ago by • 0
0
votes
3
replies
202
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 17 days ago by 41k • written 18 days ago by ▴ 20
0
votes
0
replies
94
views
Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
18 days ago Virangika • 0
0
votes
0
replies
70
views
[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
18 days ago Henry ▴ 10
1
vote
2
replies
239
views
How to retrieve detailed regression results from deseq2
DESeq2
23 days ago • updated 14 days ago Weiqian ▴ 10
0
votes
4
replies
261
views
DEG with low counts
DESeq2
updated 14 days ago by 41k • written 19 days ago by • 0
1
vote
2
replies
501
views
GSVA error
GSVA
19 days ago • updated 18 days ago Alex • 0
2
votes
3
replies
321
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
18 days ago • updated 17 days ago daniel.carbajo • 0
3
votes
3
replies
326
views
permutation test in edgeR
rna-seq edgeR
updated 12 days ago by 50k • written 25 days ago by • 0
1
vote
3
replies
345
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 18 days ago by 50k • written 23 days ago by • 0
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 18 days ago by ★ 4.1k • written 19 days ago by • 0
0
votes
1
reply
704
views
Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 21 days ago by • 0 • written 11 months ago by • 0
1
vote
2
replies
191
views
Design Matrix within group comparison more than two groups
DESeq2
21 days ago • updated 20 days ago hemantcnaik • 0
2
votes
2
replies
189
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
21 days ago julia_mcdonough • 0
2
votes
2
replies
168
views
[DiffBind] Obtaining normalization factors
DiffBind
21 days ago • updated 17 days ago Henry ▴ 10
0
votes
1
reply
131
views
Bioinformatics student
Des DESeq2
updated 21 days ago by • 0 • written 21 days ago by • 0
0
votes
0
replies
82
views
News: Important Release 3.18 Freeze Announcment
Release release Bioconductor Bioconducto
21 days ago shepherl 3.9k
2
votes
2
replies
168
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
21 days ago • updated 18 days ago daniel.carbajo • 0
0
votes
3
replies
250
views
A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 15 days ago by ▴ 850 • written 21 days ago by • 0
5
votes
9
replies
904
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
23 days ago • updated 15 days ago Chris • 0
0
votes
0
replies
90
views
Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
21 days ago Stevie Pederson • 0
2
votes
2
replies
382
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
22 days ago • updated 21 days ago Henry ▴ 10
0
votes
4
replies
220
views
Storing directories inside an ExperimentHub package?
ExperimentHub
23 days ago • updated 22 days ago Tim Barry • 0
0
votes
0
replies
97
views
News: Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing Sequencing SequencingData
22 days ago communication • 0
3
votes
6
replies
268
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
22 days ago nhaus ▴ 30
0
votes
1
reply
174
views
DESeq2 gives an error and R crashes
DESeq2
23 days ago • updated 22 days ago Shefali • 0
0
votes
0
replies
128
views
LearnTaxa with custom Silva
DECIPHER LearnTaxa
23 days ago Eryn • 0
0
votes
0
replies
85
views
queryDGIdb lexical error for some genes
lexicalerror rDGIdb DGIdb json
23 days ago Dennis • 0
0
votes
1
reply
157
views
compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 19 days ago by ★ 3.9k • written 23 days ago by • 0
8
votes
23
replies
923
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 22 days ago by ★ 3.3k • written 23 days ago by ▴ 40
0
votes
1
reply
136
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 23 days ago by ★ 4.1k • written 25 days ago by • 0
0
votes
2
replies
215
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 23 days ago by 41k • written 28 days ago by ▴ 30
0
votes
1
reply
160
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 24 days ago by 41k • written 24 days ago by • 0
0
votes
2
replies
238
views
Regressing out batch effects
DESeq2
updated 24 days ago by 41k • written 29 days ago by • 0
5
votes
6
replies
419
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 20 days ago by ★ 4.1k • written 24 days ago by ▴ 30
0
votes
1
reply
147
views
BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 24 days ago by 65k • written 24 days ago by • 0
1
vote
6
replies
485
views
GSVA on separate healthy and disease datasets
GSVA
updated 23 days ago by 65k • written 24 days ago by ▴ 60
0
votes
0
replies
106
views
ggtree tip label position (depth)
ggtree
24 days ago • updated 23 days ago Roope • 0
2
votes
6
replies
397
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
25 days ago Chris • 0
0
votes
1
reply
179
views
How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 25 days ago by 65k • written 26 days ago by • 0
0
votes
0
replies
142
views
Job: PhD-position in bioinformatics / computational biology
Mergeomics Epigenome Evolution NGS Aging
25 days ago arne.sahm • 0
0
votes
0
replies
95
views
News: Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry conference
25 days ago Wolfgang Huber ★ 13k
1,000 results • Page 3 of 20
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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. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
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…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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