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r-forge
Polychrome:Qualitative Palettes with Many Colors
Tools for creating, viewing, and assessing qualitative palettes with many (20-30 or more) colors. See Coombes and colleagues (2019) <doi:10.18637/jss.v090.c01>.
Maintained by Kevin R. Coombes. Last updated 2 months ago.
9.56 score 1.0k scripts 27 dependents
bioc
rhinotypeR:Rhinovirus genotyping
"rhinotypeR" is designed to automate the comparison of sequence data against prototype strains, streamlining the genotype assignment process. By implementing predefined pairwise distance thresholds, this package makes genotype assignment accessible to researchers and public health professionals. This tool enhances our epidemiological toolkit by enabling more efficient surveillance and analysis of rhinoviruses (RVs) and other viral pathogens with complex genomic landscapes. Additionally, "rhinotypeR" supports comprehensive visualization and analysis of single nucleotide polymorphisms (SNPs) and amino acid substitutions, facilitating in-depth genetic and evolutionary studies.
Maintained by Martha Luka. Last updated 5 months ago.
sequencinggeneticsphylogenetics
4 stars 6.20 score 2 scripts
diegommcc
SpatialDDLS:Deconvolution of Spatial Transcriptomics Data Based on Neural Networks
Deconvolution of spatial transcriptomics data based on neural networks and single-cell RNA-seq data. SpatialDDLS implements a workflow to create neural network models able to make accurate estimates of cell composition of spots from spatial transcriptomics data using deep learning and the meaningful information provided by single-cell RNA-seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> and Mañanes et al. (2024) <doi:10.1093/bioinformatics/btae072> to get an overview of the method and see some examples of its performance.
Maintained by Diego Mañanes. Last updated 5 months ago.
deconvolutiondeep-learningneural-networkspatial-transcriptomics
5 stars 4.88 score 1 scriptsbioc
clst:Classification by local similarity threshold
Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons.
Maintained by Noah Hoffman. Last updated 5 months ago.
3.78 score 10 scripts 1 dependents