0
votes
0
replies
949
views
How to use MeDIPS with BEDPE format input?
R medip-seq MEDIPS
2.9 years ago Luomeng • 0
0
votes
0
replies
1.0k
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Problem with "too large halfWindowSize" with writeMSdata after centroiding MSe data
MSnbase
2.9 years ago christine.wegler • 0
0
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1
reply
1.2k
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Samtools markdup in Rsamtools
Rsamtools
updated 2.9 years ago by 25k • written 2.9 years ago by • 0
0
votes
2
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stat_compare_means function - Error 'must have same length'
microbiomeDataSets Microbiome
2.9 years ago Elif • 0
1
vote
0
replies
2.9k
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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 2.8 years ago by ▴ 10 • written 2.9 years ago by ▴ 10
2
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2
replies
1.9k
views
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
DEXSeq
2.9 years ago Ben J ▴ 20
0
votes
2
replies
981
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Categorical or continuous covariates
ALL The DifferentialRegulation PathNet
written 2.9 years ago by • 0
4
votes
5
replies
1.6k
views
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
2.9 years ago Robert Castelo ★ 3.4k
0
votes
1
reply
1.1k
views
input for singR function
Seurat_object singe-cell singleR
updated 11 months ago by • 0 • written 2.9 years ago by • 0
0
votes
0
replies
865
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rnbeads inference
epigenetics RnBeads
2.9 years ago Jitendra ▴ 10
0
votes
0
replies
1.0k
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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
762
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 21 months ago by • 0 • written 2.9 years ago by • 0
0
votes
1
reply
970
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
841
views
rtracklayer ignores ranges argument
rtracklayer
2.9 years ago Kyle • 0
0
votes
0
replies
989
views
Changing pathway names in pathway analysis
pathways Pathways
2.9 years ago Katharina • 0
0
votes
0
replies
947
views
Analyze Amplicon Seq results for variants and mutation sites
virus pcr amplican mutations
2.9 years ago Sara • 0
0
votes
0
replies
576
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customProDB: error aberrant fasta from SNV
customProDB
2.9 years ago finoa.li • 0
0
votes
1
reply
990
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
707
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
712
views
Distance between columns vs distance between rows and SVD
distance svd
3.0 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 3.0 years ago by • 0
0
votes
1
reply
877
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 3.0 years ago by • 0
0
votes
0
replies
1.8k
views
GOplots::GOChord with heatmaps?
GOChord ggplot2::geom_polygon() GOplot ggplot2
3.0 years ago adrija.kalvisa • 0
0
votes
0
replies
781
views
Rsubread align every slow in mac but faster in windows
Rsubread
3.0 years ago Wei • 0
0
votes
0
replies
658
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msa module crash
msa
3.0 years ago systems • 0
0
votes
1
reply
3.0k
views
convert local downloaded bigwig files to .bed files
BRgen BRGenomics
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by ▴ 30
4
votes
8
replies
4.6k
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 3.0 years ago by ▴ 10
0
votes
0
replies
598
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INSPEcT: How to get the RNA dynamics for steady-state with INSPEcT minus
INSPEcT
3.0 years ago MK • 0
0
votes
0
replies
1.0k
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Does verboseScatterplot in WGCNA package allow for highlighting a subset of genes
WGCNA
3.0 years ago S • 0
0
votes
1
reply
1.1k
views
GRanges list convert into igraph format
GRanges igraph
updated 3.0 years ago by ▴ 760 • written 3.0 years ago by ▴ 670
0
votes
0
replies
1.1k
views
Error importing UCSC phastCons annotation in BigWig format
GenomicRanges rtracklayer
3.0 years ago Delta._.43 ▴ 20
1
vote
1
reply
792
views
MSc student
genomes
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
0
votes
8
replies
2.7k
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DropletUtils::read10xCounts error
read10xCounts DropletUtils
3.0 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 3.0 years ago by 68k • written 3.0 years ago by • 0
0
votes
0
replies
993
views
adding peptides to a multiple sequence alignment
msa IRanges Biostrings
3.0 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
3.0 years ago Arend ▴ 10
0
votes
1
reply
1.1k
views
Error in ATACseqQC bamQC analysis
ATACSeq ATACseqQC
updated 3.0 years ago by ★ 1.3k • written 3.0 years ago by • 0
0
votes
1
reply
1.4k
views
cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
updated 3.0 years ago by ▴ 160 • written 3.0 years ago by ▴ 10
0
votes
2
replies
831
views
Time series between two conditions with a common time zero
timeseries
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
votes
0
replies
583
views
KEGGREST API keggLink and keggGet for hsa:5164
reactions hsa:5164
3.0 years ago susrinivasan • 0
0
votes
8
replies
2.0k
views
Question about Diffbind counts
DiffBind
3.0 years ago slrpatty • 0
0
votes
0
replies
1.5k
views
Trying to use a NanoString expression set with batch effects to do GSVA
GSVA Normalization BatchEffect GSVAdata NanoString
3.0 years ago Zhijie • 0
0
votes
1
reply
877
views
Could not find XtraSNPlocs.Hsapiens.dbSNP155.GRCh37/GRCh38 packages
XtraSNPlocs SNPlocs
updated 3.0 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
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3.0 years ago Lluís Revilla Sancho ▴ 760
0
votes
2
replies
1.2k
views
Celfiles not reading in
Microarray
written 3.0 years ago by • 0
0
votes
1
reply
1.1k
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
0
votes
0
replies
1.2k
views
Avoid end gap penalty in Biostrings::pairwiseAlignment
Alignment Biostrings
3.0 years ago vonSkopnik • 0
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Comment: Ensembl plants at annotationHub? by jwp48 • 0
Nope I don't mind haha! Anyway thanks so much! Thats super kind of you!
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Hi Andrew, We don't have that much experience combining different datasets with limpa yet, but my feeling is that the same DPC should be u…
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Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
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Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
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Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
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