0
votes
1
reply
1.7k
views
WGCNA soft thresholding suggesting a power of 1
independence thresholding WGCNA connectivity scale
updated 21 months ago by ▴ 740 • written 2.9 years ago by • 0
0
votes
0
replies
931
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
2.9 years ago Luomeng • 0
0
votes
0
replies
991
views
Problem with "too large halfWindowSize" with writeMSdata after centroiding MSe data
MSnbase
2.9 years ago christine.wegler • 0
0
votes
1
reply
1.2k
views
Samtools markdup in Rsamtools
Rsamtools
updated 2.9 years ago by 25k • written 2.9 years ago by • 0
0
votes
2
replies
3.0k
views
stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
2.9 years ago Elif • 0
1
vote
0
replies
2.9k
views
Convert SpatialExperiment Object to Seurat Object
scuttle scater seurat SpatialExperiment
2.9 years ago cathalgking ▴ 10
1
vote
1
reply
1.1k
views
BiocGenerics package: 404 error during R shiny app deployment
BiocGenerics ddCt
updated 2.7 years ago by ▴ 10 • written 2.9 years ago by ▴ 10
2
votes
2
replies
1.8k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.9 years ago Ben J ▴ 20
0
votes
2
replies
968
views
Categorical or continuous covariates
ALL The DifferentialRegulation PathNet
written 2.9 years ago by • 0
4
votes
5
replies
1.5k
views
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
2.9 years ago • updated 2.8 years ago Robert Castelo ★ 3.4k
0
votes
1
reply
1.1k
views
input for singR function
Seurat_object singe-cell singleR
updated 10 months ago by • 0 • written 2.9 years ago by • 0
0
votes
0
replies
848
views
rnbeads inference
epigenetics RnBeads
2.9 years ago Jitendra ▴ 10
0
votes
0
replies
979
views
model overfitting using OPLS DA for metabolomics analysis
OPLSDA
updated 2.9 years ago by 4.2k • written 2.9 years ago by • 0
0
votes
0
replies
755
views
Numbers of Signaling Pathways?
chemistry
2.9 years ago beikrystal25 • 0
0
votes
1
reply
1.1k
views
Cibersort phenotype file
cibersort deconvR immune
updated 20 months ago by • 0 • written 2.9 years ago by • 0
0
votes
1
reply
941
views
AnnotationForge::makeOrgPackageFromNCBI - ERROR to access url (NCBI FTP site)
AnnotationForge
updated 2.9 years ago by • 0 • written 2.9 years ago by ▴ 10
0
votes
0
replies
823
views
rtracklayer ignores ranges argument
rtracklayer
2.9 years ago Kyle • 0
0
votes
0
replies
969
views
Changing pathway names in pathway analysis
pathways Pathways
2.9 years ago Katharina • 0
0
votes
0
replies
924
views
Analyze Amplicon Seq results for variants and mutation sites
virus pcr amplican mutations
2.9 years ago Sara • 0
0
votes
0
replies
565
views
customProDB: error aberrant fasta from SNV
customProDB
2.9 years ago finoa.li • 0
0
votes
1
reply
967
views
Bioconductor tool for curating annotations?
Annotation
updated 2.9 years ago by ▴ 760 • written 2.9 years ago by ▴ 180
1
vote
0
replies
695
views
Alternatives to perform peptide identification in Bioconductor version '3.16'?
peptide peptideidentification rTANDEM MSGFplus Alternatives
updated 2.9 years ago by 4.2k • written 2.9 years ago by ▴ 10
0
votes
0
replies
685
views
Distance between columns vs distance between rows and SVD
distance svd
2.9 years ago Lenny186 • 0
0
votes
1
reply
1.3k
views
Splicing analysis with ASpli package gives an error when I use binGenome function.
S4Vectors Aspli
updated 2.9 years ago by • 0 • written 2.9 years ago by • 0
0
votes
1
reply
870
views
In WGCNA which is the matrix on which the eigen decomposition is run to get the module eigen gene
WGCNA
updated 2.9 years ago by ▴ 50 • written 2.9 years ago by • 0
0
votes
0
replies
1.8k
views
GOplots::GOChord with heatmaps?
GOChord ggplot2::geom_polygon() GOplot ggplot2
2.9 years ago adrija.kalvisa • 0
0
votes
0
replies
765
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.9 years ago Wei • 0
0
votes
0
replies
644
views
msa module crash
msa
2.9 years ago systems • 0
0
votes
1
reply
2.9k
views
convert local downloaded bigwig files to .bed files
BRgen BRGenomics
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by ▴ 30
4
votes
8
replies
4.5k
views
How to normalize long-read RNA-seq data for comparison with short-reads
NanoporeRNASeq LongRead Normalization ShortRead IlluminaRNASeq
updated 17 months ago by • 0 • written 2.9 years ago by ▴ 10
0
votes
0
replies
583
views
INSPEcT: How to get the RNA dynamics for steady-state with INSPEcT minus
INSPEcT
2.9 years ago MK • 0
0
votes
0
replies
994
views
Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
2.9 years ago S • 0
0
votes
1
reply
1.1k
views
GRanges list convert into igraph format
GRanges igraph
updated 2.9 years ago by ▴ 760 • written 2.9 years ago by ▴ 670
0
votes
0
replies
1.1k
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
2.9 years ago Delta._.43 ▴ 20
1
vote
1
reply
778
views
MSc student
genomes
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
0
votes
8
replies
2.6k
views
DropletUtils::read10xCounts error
read10xCounts DropletUtils
2.9 years ago fdumetz • 0
0
votes
3
replies
1.6k
views
Error when using "readTranscriptFeatures" in "Genomation" R package for loading the bed file
readTranscriptFeatures R genomation bed
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
votes
0
replies
978
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
2.9 years ago Mario Dejung • 0
1
vote
0
replies
1.1k
views
Problem with VSN: Error in vsnML(sv) : L-BFGS-B needs finite values of 'fn'
justvsn vsn Normalization vsn2 Proteomics
2.9 years ago Arend ▴ 10
0
votes
1
reply
1.1k
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 2.9 years ago by ★ 1.3k • written 2.9 years ago by • 0
0
votes
1
reply
1.4k
views
cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
updated 2.9 years ago by ▴ 160 • written 2.9 years ago by ▴ 10
0
votes
2
replies
816
views
Time series between two conditions with a common time zero
timeseries
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
0
votes
0
replies
578
views
KEGGREST API keggLink and keggGet for hsa:5164
reactions hsa:5164
2.9 years ago susrinivasan • 0
0
votes
8
replies
2.0k
views
Question about Diffbind counts
DiffBind
2.9 years ago slrpatty • 0
0
votes
0
replies
1.4k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
2.9 years ago Zhijie • 0
0
votes
1
reply
868
views
Could not find XtraSNPlocs.Hsapiens.dbSNP155.GRCh37/GRCh38 packages
XtraSNPlocs SNPlocs
updated 2.9 years ago by ★ 5.0k • written 3.0 years ago by ▴ 20
0
votes
0
replies
1.1k
views
Identify accepted columns in TxDb objects
TxDb
3.0 years ago • updated 2.9 years ago Lluís Revilla Sancho ▴ 760
0
votes
2
replies
1.1k
views
Celfiles not reading in
Microarray
written 3.0 years ago by • 0
0
votes
1
reply
1.0k
views
GSA type of input data
GSEA GSA vst
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 70
1
vote
0
replies
1.3k
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
3.0 years ago r_grau ▴ 10
1,000 results • Page 15 of 20
Recent ...
Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to Michael Love 43k
Popular Question to Luca • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to James W. MacDonald 68k
Locations • All
Italy, 3 minutes ago
Germany, 2 hours ago
United States, 2 hours ago
United States, 2 hours ago
WEHI, Melbourne, Australia, 2 hours ago
Traffic: 982 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