1
vote
1
reply
182
views
Differentially expressed genes in monocle pseudotime
monocle
updated 16 days ago by 50k • written 18 days ago by • 0
4
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8
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386
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Memory errors using read.bismark?
dmrseq bsseq
updated 14 days ago by ▴ 740 • written 21 days ago by • 0
3
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3
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197
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Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array BiocGenerics BiocParallel Biobase
20 days ago • updated 14 days ago jacques.imbert • 0
0
votes
1
reply
137
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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
votes
3
replies
200
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by 41k • written 17 days ago by ▴ 20
0
votes
0
replies
93
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Diffbind Error in socketConnection
DiffBind Errorinsocketconnection SpikeIn
17 days ago Virangika • 0
0
votes
0
replies
70
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
17 days ago Henry ▴ 10
1
vote
2
replies
239
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How to retrieve detailed regression results from deseq2
DESeq2
22 days ago • updated 13 days ago Weiqian ▴ 10
0
votes
4
replies
260
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DEG with low counts
DESeq2
updated 13 days ago by 41k • written 18 days ago by • 0
1
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2
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489
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GSVA error
GSVA
18 days ago • updated 17 days ago Alex • 0
2
votes
3
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321
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ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
17 days ago • updated 16 days ago daniel.carbajo • 0
3
votes
3
replies
323
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permutation test in edgeR
rna-seq edgeR
updated 11 days ago by 50k • written 24 days ago by • 0
1
vote
3
replies
343
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 17 days ago by 50k • written 22 days ago by • 0
0
votes
1
reply
128
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Deseq2 Rlog transformation
DESeq2
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
0
votes
1
reply
700
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 20 days ago by • 0 • written 11 months ago by • 0
1
vote
2
replies
189
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Design Matrix within group comparison more than two groups
DESeq2
20 days ago • updated 19 days ago hemantcnaik • 0
2
votes
2
replies
188
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
20 days ago julia_mcdonough • 0
2
votes
2
replies
166
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[DiffBind] Obtaining normalization factors
DiffBind
20 days ago • updated 16 days ago Henry ▴ 10
0
votes
1
reply
130
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Bioinformatics student
Des DESeq2
updated 20 days ago by • 0 • written 20 days ago by • 0
0
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0
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81
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News: Important Release 3.18 Freeze Announcment
Release release Bioconductor Bioconducto
20 days ago shepherl 3.9k
2
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2
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167
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ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
20 days ago • updated 17 days ago daniel.carbajo • 0
0
votes
3
replies
249
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A ComBat-seq issue: the covariates are confounded
ComBat-seq sva
updated 14 days ago by ▴ 850 • written 20 days ago by • 0
5
votes
9
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899
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Light difference when using coef vs omit a group when compare 3 groups.
limma
22 days ago • updated 14 days ago Chris • 0
0
votes
0
replies
88
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Cannot use `readVcf()` on a file created with `writeVcf()`
VariantAnnotation
20 days ago Stevie Pederson • 0
2
votes
2
replies
379
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[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind Normalization
21 days ago • updated 20 days ago Henry ▴ 10
0
votes
4
replies
220
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Storing directories inside an ExperimentHub package?
ExperimentHub
22 days ago • updated 21 days ago Tim Barry • 0
0
votes
0
replies
97
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News: Course Manipulation of NGS Data for Genomic and Population Genetics Analyses
sequencing Sequencing SequencingData
21 days ago communication • 0
3
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6
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265
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Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
21 days ago nhaus ▴ 30
0
votes
1
reply
173
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DESeq2 gives an error and R crashes
DESeq2
22 days ago • updated 21 days ago Shefali • 0
0
votes
0
replies
127
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LearnTaxa with custom Silva
DECIPHER LearnTaxa
22 days ago Eryn • 0
0
votes
0
replies
85
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queryDGIdb lexical error for some genes
lexicalerror rDGIdb DGIdb json
22 days ago Dennis • 0
0
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1
reply
157
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compareCluster dotplot: how to modify the genesets order
DOSE enrichplot clusterProfiler
updated 18 days ago by ★ 3.9k • written 22 days ago by • 0
8
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23
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914
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Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment ExpressionSet
updated 21 days ago by ★ 3.3k • written 22 days ago by ▴ 40
0
votes
1
reply
133
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Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 22 days ago by ★ 4.1k • written 24 days ago by • 0
0
votes
2
replies
214
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 23 days ago by 41k • written 27 days ago by ▴ 30
0
votes
1
reply
158
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 23 days ago by 41k • written 23 days ago by • 0
0
votes
2
replies
233
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Regressing out batch effects
DESeq2
updated 23 days ago by 41k • written 28 days ago by • 0
5
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6
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416
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 19 days ago by ★ 4.1k • written 23 days ago by ▴ 30
0
votes
1
reply
146
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BAM write error in HTSeqGenie
HTSeqGenie BAM
updated 23 days ago by 65k • written 23 days ago by • 0
1
vote
6
replies
481
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GSVA on separate healthy and disease datasets
GSVA
updated 22 days ago by 65k • written 23 days ago by ▴ 60
0
votes
0
replies
106
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ggtree tip label position (depth)
ggtree
23 days ago • updated 22 days ago Roope • 0
2
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6
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391
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How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
24 days ago Chris • 0
0
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1
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177
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How can I create a GO plot with ggpubr and clusterProfiler libraries (begginer)
clusterProfiler ggpubr
updated 24 days ago by 65k • written 25 days ago by • 0
0
votes
0
replies
140
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Job: PhD-position in bioinformatics / computational biology
Mergeomics Epigenome Evolution NGS Aging
24 days ago arne.sahm • 0
0
votes
0
replies
94
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News: Call for proposals: European CarpentryConnect - 12-14 November 2024, at EMBL Heidelberg
carpentry conference
24 days ago Wolfgang Huber ★ 13k
1
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10
replies
445
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Obtaining pheno data from CEL files
GEO affy
4 weeks ago • updated 23 days ago Kurtis • 0
0
votes
1
reply
157
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Limma design matrix only showing 3/4 treatments?
limma designmatrix
updated 26 days ago by 50k • written 27 days ago by • 0
1
vote
3
replies
241
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 27 days ago by 65k • written 27 days ago by • 0
1
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2
replies
224
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MethylKit read issue
methylKit
updated 27 days ago by 65k • written 4 weeks ago by • 0
1
vote
2
replies
3.1k
views
Extract genes from ggvenn?
ggvenn
updated 27 days ago by ▴ 10 • written 2.0 years ago by • 0
45,611 results • Page 3 of 913
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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