5
votes
6
replies
2.9k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 22 days ago by 66k • written 2.4 years ago by • 0
1
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2
replies
301
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
15 days ago • updated 14 days ago Dylan.Sheerin • 0
2
votes
3
replies
306
views
package goseq seems to be not available on the latest version of R
goseq
updated 18 days ago by 50k • written 21 days ago by ▴ 20
1
vote
1
reply
162
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 24 days ago by 42k • written 24 days ago by • 0
1
vote
3
replies
145
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 4 days ago by 66k • written 5 days ago by ▴ 720
1
vote
8
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147
views
Slightly different count plots from R and spreadsheet
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2 days ago boczniak767 ▴ 720
2
votes
1
reply
102
views
How to design DEXSeq formula for multiple variables
DEXSeq
updated 9 days ago by ★ 1.9k • written 11 days ago by • 0
2
votes
3
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1.8k
views
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
chipqc
updated 11 days ago by • 0 • written 3.6 years ago by ▴ 60
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA gene set testing vooma limma voom gsea
updated 16 days ago by ▴ 10 • written 7.4 years ago by ▴ 190
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 16 days ago by 50k • written 5.6 years ago by ▴ 10
0
votes
1
reply
123
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 10 days ago by 42k • written 11 days ago by • 0
1
vote
1
reply
89
views
Control group between 2 batches have different expression in RNAseq data
BatchQC BatchEffect rnaseqGene Normalization
updated 4 days ago by 66k • written 4 days ago by • 0
2
votes
4
replies
143
views
Help with infinite recursion - non-zero exit status in installation of GenomeInfoDbData
Install GenomeInfoDbData GenomeInfoDb
updated 1 day ago by 66k • written 2 days ago by ▴ 20
15
votes
23
replies
2.1k
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The difference when using Limma compare between 3 conditions vs 2 conditions
limma
8 weeks ago • updated 24 days ago Chris ▴ 10
2
votes
2
replies
71
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Get gene symbols for a set of hg19 coordinates
annotation hg19
2 days ago • updated 1 day ago pcantalupo ▴ 10
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 14 days ago by • 0 • written 16 months ago by ▴ 10
0
votes
2
replies
50
views
Cluster columns in Pheatmap
geneexp pheatmap heatmaps cluster
updated 11 hours ago by 66k • written 14 hours ago by • 0
1
vote
1
reply
190
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 4 days ago by 66k • written 4 days ago by • 0
1
vote
2
replies
222
views
Citation for edgeR user guide
edgeR
written 4 weeks ago by ▴ 30
0
votes
2
replies
969
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using WGCNA, positive or negative corrlation between genes composing modules.
correlation wgcna network
updated 9 days ago by • 0 • written 18 months ago by • 0
0
votes
3
replies
286
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 24 days ago by 66k • written 25 days ago by • 0
0
votes
1
reply
39
views
Error when running topGO with KS statistic and elim agorithm
topGO
updated 10 hours ago by 66k • written 1 day ago by • 0
1
vote
1
reply
160
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 28 days ago by ▴ 40 • written 28 days ago by ★ 1.5k
1
vote
2
replies
315
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
24 days ago • updated 23 days ago Yveto • 0
0
votes
2
replies
181
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
24 days ago • updated 21 days ago Aurora • 0
0
votes
2
replies
763
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Query regarding phyloseq object construct with QIIME output
phyloseq microbiome Metagenomics
updated 9 days ago by • 0 • written 11 months ago by • 0
2
votes
5
replies
281
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How to retrieve gene ontology GO class from gene list?
GO.db goTools
updated 29 days ago by 66k • written 4 weeks ago by • 0
5
votes
6
replies
298
views
Not able to install any Bioconductor 3.18 package [unable to access index]
Install
updated 1 day ago by ▴ 120 • written 1 day ago by ▴ 140
0
votes
1
reply
143
views
putting my own expression data in deseq2
DESeq2
updated 24 days ago by ★ 4.2k • written 24 days ago by • 0
0
votes
0
replies
143
views
Empty table plot using plotGseaTable()
fgsea
23 days ago • updated 21 days ago Chris ▴ 10
0
votes
0
replies
99
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News: BioC2024 deadlines approaching
BioC2024 Bioconductor Community
24 days ago Maria Doyle ▴ 70
0
votes
0
replies
38
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FindOverlaps, makeVennDiagram and "others"
ATACSeq peaks ATAC ChIPpeakAnno
3 days ago Raghad • 0
1
vote
0
replies
86
views
News: Ensembl 112 has been released.
ensembldb biomaRt ensemblrelease
10 days ago Aleena ▴ 30
0
votes
0
replies
99
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DiffBind: no peaks in DBA object
DiffBind macs2 chipseq
22 days ago yvonneh • 0
0
votes
0
replies
91
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
22 days ago Ian D. ▴ 70
0
votes
0
replies
103
views
how to do Differential splicing from SGSeq analysis
DEXSeq SGSeq
4 weeks ago • updated 25 days ago Sara • 0
0
votes
0
replies
31
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Job: Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod Evolution QuantitativeTrailLocus Genetics JobPosting
4 days ago pierre.devillemereuil • 0
0
votes
0
replies
40
views
Processing of curatedmetagenomics
curatedMetagenomicData
4 days ago Edward • 0
0
votes
4
replies
64
views
Cannot install oligo on Fedora
oligo source Install
updated 4 hours ago by 66k • written 9 hours ago by ★ 4.0k
0
votes
0
replies
96
views
ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
8 days ago Anton01 • 0
0
votes
0
replies
36
views
Conditional analysis
GENESIS
3 days ago SuperDad • 0
0
votes
7
replies
340
views
ChAMP installation issue
Cha ChAMP
updated 2 days ago by 66k • written 11 days ago by • 0
4
votes
3
replies
1.0k
views
BayesSpace parameters for DLPFC Visium data
BayesSpace
written 3.1 years ago by ▴ 30
0
votes
0
replies
91
views
Recommendations on deploying cytoviewer shiny.appobj to shinyapps.io?
cytoviewer ShinyApps
15 days ago neilzhao ▴ 30
0
votes
0
replies
30
views
Problem in execuation of filterAndTrim command in DADA2
Bioconductor dada2
2 days ago • updated 1 day ago abhisek001 • 0
0
votes
0
replies
101
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
25 days ago Chris ▴ 10
0
votes
0
replies
56
views
Minor allele data from grch38 giving NAs from getBM ?
BioMartGOGeneSets allele_freq biomaRt getBM
6 days ago • updated 5 days ago Abiologist • 0
0
votes
0
replies
126
views
dba.plotProfile() plotting and interpretation
DiffBind
21 days ago Henry ▴ 10
0
votes
0
replies
12
views
Spam: Understanding Laser Hair Removal?
healthyControlsPresenceChecker
4 days ago shahrozimmac 0
0
votes
1
reply
732
views
How to arrange multiple plots into one page in NOISeq?
noiseq RNA-seq quality control
updated 3 days ago by • 0 • written 4.7 years ago by ▴ 80
181 results • Page 3 of 4
Recent ...
Replies
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Answer: GSVA function by Robert Castelo ★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Comment: Cannot install oligo on Fedora by Guido Hooiveld ★ 4.0k
Aha, that is a good one! Starting from release 40, as I just found out, Fedora apparently is not including/using `zlib` as such anymore, b…
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Answer: How to run allelic imbalance in apeglm
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
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