2
votes
15
replies
731
views
Problems with enrichGO
clusterProfiler enrichGO
updated 3 months ago by 42k • written 3 months ago by • 0
2
votes
13
replies
481
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
27 days ago • updated 24 days ago fernanda.backsouza ▴ 10
2
votes
10
replies
1.2k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
6 months ago rohitsatyam102 ▴ 20
0
votes
8
replies
387
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 24 days ago by ★ 1.4k • written 25 days ago by • 0
2
votes
8
replies
2.4k
views
Reading HDF5 Files In The Cloud
Rhdf5lib rhdf5
3.2 years ago • updated 9 months ago Thomas Sandmann ▴ 90
0
votes
7
replies
690
views
Deleted:No significant MVPs with a BH adjusted P-value below 0.05
ChAMP
updated 5 months ago by ▴ 780 • written 5 months ago by • 0
1
vote
7
replies
1.9k
views
Error using champ.import
ChAMP EPICv2
updated 4 weeks ago by • 0 • written 10 months ago by • 0
0
votes
7
replies
438
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages Proxy Bioconductor GEOquery Internet_connection_problem
7 weeks ago • updated 6 weeks ago needNGS • 0
8
votes
7
replies
1.2k
views
Why is DMRcate not available for Bioconductor version 3.18?
DMRcate
written 5 months ago by ▴ 30
2
votes
7
replies
382
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
10 days ago • updated 7 days ago sajadahmad41454 • 0
0
votes
6
replies
790
views
StringDB: Cannot finish their tutorial because of an error
STRINGdb
updated 9 weeks ago by • 0 • written 12 weeks ago by • 0
2
votes
6
replies
1.1k
views
Looking for documentation about the use of "split = .sign" in enrichplot's dotplot
enrichplot
3 months ago • updated 12 weeks ago Tobias • 0
0
votes
6
replies
856
views
Merge 2 accounts, or delete 1 account.
Bioconductor ALL
11 months ago simone.tiberi • 0
0
votes
6
replies
960
views
flowCore >2.0 read.FCS results in $SPILLOVER error when reading certain FCS files (could it be a warning?)
read.FCS flowCore
updated 5 months ago by ▴ 350 • written 5 months ago by • 0
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 4 months ago by ★ 4.0k • written 14 months ago by ▴ 10
2
votes
6
replies
464
views
How to make boxplot with pairwise and overall p value from Limma
t.test boxplot limma anova
5 weeks ago Chris ▴ 10
0
votes
6
replies
727
views
fastMNN reproducibility across machines when using Docker
batchelor
10 months ago nils.eling • 0
3
votes
6
replies
306
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq sva
5 weeks ago nhaus ▴ 30
0
votes
5
replies
2.3k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts SAM htseqcounts
updated 10 months ago by ▴ 380 • written 7.0 years ago by • 0
3
votes
5
replies
1.2k
views
why is downloading the .tar.gz file for a given bioconductor package, then installing with R CMD INSTALL so much more effective than BiocManager::ins…
Bioconductor Install library biocmanager
updated 10 months ago by 6.7k • written 10 months ago by ▴ 20
0
votes
5
replies
765
views
R for Mass Spectrometry: PSMatch package won't read .mzid file exported from ProteinPilot?
RforProteomics Proteomics ProteomicsWorkflow
updated 9 months ago by 1.6k • written 9 months ago by • 0
0
votes
5
replies
1.0k
views
What to whitelist in Firewall to allow downloading packages
Bioconductor NetworkInference
updated 10 months ago by 3.9k • written 10 months ago by • 0
1
vote
5
replies
368
views
fgsea fork
fgsea
updated 7 weeks ago by 65k • written 7 weeks ago by • 0
1
vote
5
replies
883
views
DEXSeq output included non-exist exons
DEXSeq exon_definition exon
updated 10 months ago by ★ 1.9k • written 10 months ago by • 0
0
votes
5
replies
2.1k
views
How can I limit the number of displayed genes in heatplot
heatplot enrichplot
updated 8 months ago by • 0 • written 17 months ago by • 0
1
vote
5
replies
484
views
BiomaRt download data error
biomaRt
updated 3 months ago by ★ 6.5k • written 3 months ago by • 0
1
vote
4
replies
768
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 11 months ago by 16k • written 12 months ago by • 0
1
vote
4
replies
313
views
EDAseq to normalise for both gene-length and GC-content
norma EDASeq EDA Normalization
8 weeks ago samuel.channon • 0
2
votes
4
replies
549
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 4 months ago by 50k • written 5 months ago by • 0
0
votes
4
replies
267
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago • updated 29 days ago lonn • 0
0
votes
4
replies
320
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks Survival
updated 3 months ago by ▴ 730 • written 3 months ago by • 0
0
votes
4
replies
590
views
Retrieve gene ontologies (GO) for genes and a species by REST API
GO ensembldb
7 months ago • updated 6 months ago Rockbar • 0
0
votes
4
replies
325
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
2
votes
4
replies
1.3k
views
DiffBind: dba.plotProfile(profiles)
DiffBind
updated 3 months ago by • 0 • written 2.4 years ago by • 0
0
votes
4
replies
409
views
Installation problem of rtracklayer on Bioconductor version 3.19
newpackage rtracklayer
updated 12 weeks ago by 3.9k • written 12 weeks ago by • 0
0
votes
4
replies
695
views
Mfuzz package loading issues
Mfuzz loadingissues macbook
6 months ago Jon • 0
0
votes
4
replies
952
views
Limma multi-group, nested analysis with aggregation
limma
12 months ago • updated 9 months ago Jonathan ▴ 10
1
vote
4
replies
1.8k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR SeuratscRNA
written 5 months ago by ▴ 40
1
vote
4
replies
505
views
EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
3 months ago mikat • 0
2
votes
4
replies
3.8k
views
How to convert large gene counts data into matrix?
R Bioconductor singlecell bioinformatics seurat
updated 3 months ago by 50k • written 4.8 years ago by • 0
2
votes
4
replies
623
views
BiocGenerics binary is outdated for macOS ARM
BiocGenerics
11 months ago Michael Steinbaugh ▴ 90
0
votes
4
replies
1.0k
views
GDCdownload Directory Problem :(
TCGAWorkflowData TCGAbiolinks
updated 12 weeks ago by 700 • written 2.1 years ago by • 0
0
votes
4
replies
594
views
Pairwise comparison for DEG analysis
limma
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
1
vote
4
replies
1.1k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
11 months ago Jiyoung Lee • 0
0
votes
3
replies
270
views
problems updating package
TrajectoryGeometry
12 weeks ago michael.shapiro • 0
0
votes
3
replies
224
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
0
votes
3
replies
1.5k
views
Not able to install clusterProfiler
clusterProfiler
updated 3 months ago by • 0 • written 10 months ago by • 0
0
votes
3
replies
96
views
STRINGdb : error with string_db$plot_network()
STRINGdb
updated 1 day ago by ▴ 80 • written 1 day ago by • 0
0
votes
3
replies
783
views
How to plot gene names in Gviz plotTracks and get the ideogram track to work (US-based)?
gviz Saccharomyces_cerevisiae Gviz ideogram
updated 8 months ago by ▴ 730 • written 8 months ago by • 0
0
votes
3
replies
556
views
Suggested package missing from Development version of Bioconductor
Devel
updated 7 months ago by 3.9k • written 7 months ago by • 0
400 results • Page 1 of 8
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards • All
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Locations • All
The city by the bay, 9 minutes ago
WEHI, Melbourne, Australia, 23 minutes ago
Sweden, 32 minutes ago
Melbourne, Australia, 45 minutes ago
Hong Kong, 2 hours ago
Traffic: 373 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6