Showing 90 of total 90 results (show query)
immunomind
immunarch:Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq) and single-cell sequencing (scRNAseq). Immunarch implements most of the widely used AIRR analysis methods, such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor databases and clonotype tracking in vaccination and cancer studies. A successor to our previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
Maintained by Vadim I. Nazarov. Last updated 12 months ago.
airr-analysisb-cell-receptorbcrbcr-repertoirebioinformaticsigig-repertoireimmune-repertoireimmune-repertoire-analysisimmune-repertoire-dataimmunoglobulinimmunoinformaticsimmunologyrep-seqrepertoire-analysissingle-cellsingle-cell-analysist-cell-receptortcrtcr-repertoirecpp
49.5 match 315 stars 9.49 score 203 scripts
bioc
IgGeneUsage:Differential gene usage in immune repertoires
Detection of biases in the usage of immunoglobulin (Ig) genes is an important task in immune repertoire profiling. IgGeneUsage detects aberrant Ig gene usage between biological conditions using a probabilistic model which is analyzed computationally by Bayes inference. With this IgGeneUsage also avoids some common problems related to the current practice of null-hypothesis significance testing.
Maintained by Simo Kitanovski. Last updated 5 months ago.
differentialexpressionregressiongeneticsbayesianbiomedicalinformaticsimmunooncologymathematicalbiologyb-cell-receptorbcr-repertoiredifferential-analysisdifferential-gene-expressionhigh-throughput-sequencingimmune-repertoireimmune-repertoire-analysisimmune-repertoiresimmunogenomicsimmunoglobulinimmunoinformaticsimmunological-bioinformaticsimmunologytcr-repertoirevdj-recombinationcpp
26.9 match 6 stars 5.92 score 1 scriptsbioc
easier:Estimate Systems Immune Response from RNA-seq data
This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input. We integrate RNA-seq data with different types of prior knowledge to extract quantitative descriptors of the tumor microenvironment from several points of view, including composition of the immune repertoire, and activity of intra- and extra-cellular communications. Then, we use multi-task machine learning trained in TCGA data to identify how these descriptors can simultaneously predict several state-of-the-art hallmarks of anti-cancer immune response. In this way we derive cancer-specific models and identify cancer-specific systems biomarkers of immune response. These biomarkers have been experimentally validated in the literature and the performance of EaSIeR predictions has been validated using independent datasets form four different cancer types with patients treated with anti-PD1 or anti-PDL1 therapy.
Maintained by Oscar Lapuente-Santana. Last updated 5 months ago.
geneexpressionsoftwaretranscriptionsystemsbiologypathwaysgenesetenrichmentimmunooncologyepigeneticsclassificationbiomedicalinformaticsregressionexperimenthubsoftware
33.6 match 4.20 score 16 scripts
pharmacologie-caen
vigicaen:'VigiBase' Pharmacovigilance Database Toolbox
Perform the analysis of the World Health Organization (WHO) Pharmacovigilance database 'VigiBase' (Extract Case Level version), <https://who-umc.org/> e.g., load data, perform data management, disproportionality analysis, and descriptive statistics. Intended for pharmacovigilance routine use or studies. This package is NOT supported nor reflect the opinion of the WHO, or the Uppsala Monitoring Centre. Disproportionality methods are described by Norén et al (2013) <doi:10.1177/0962280211403604>.
Maintained by Charles Dolladille. Last updated 3 days ago.
datamanagementpharmacovigilance
20.5 match 1 stars 6.27 score 11 scripts
qile0317
APackOfTheClones:Visualization of Clonal Expansion for Single Cell Immune Profiles
Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.
Maintained by Qile Yang. Last updated 4 months ago.
clonal-analysisimmune-repertoireimmune-systemscrna-seqscrnaseqseuratsingle-cellsingle-cell-genomicscpp
17.9 match 15 stars 6.45 score 15 scriptsbioc
SingleCellAlleleExperiment:S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes
Defines a S4 class that is based on SingleCellExperiment. In addition to the usual gene layer the object can also store data for immune genes such as HLAs, Igs and KIRs at allele and functional level. The package is part of a workflow named single-cell ImmunoGenomic Diversity (scIGD), that firstly incorporates allele-aware quantification data for immune genes. This new data can then be used with the here implemented data structure and functionalities for further data handling and data analysis.
Maintained by Jonas Schuck. Last updated 2 months ago.
datarepresentationinfrastructuresinglecelltranscriptomicsgeneexpressiongeneticsimmunooncologydataimport
17.2 match 7 stars 6.30 score 12 scripts
mlizhangx
NAIR:Network Analysis of Immune Repertoire
Pipelines for studying the adaptive immune repertoire of T cells and B cells via network analysis based on receptor sequence similarity. Relate clinical outcomes to immune repertoires based on their network properties, or to particular clusters and clones within a repertoire. Yang et al. (2023) <doi:10.3389/fimmu.2023.1181825>.
Maintained by Brian Neal. Last updated 2 months ago.
15.2 match 7 stars 6.83 score 27 scripts
ajitjohnson
imsig:Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours
Estimate the relative abundance of tissue-infiltrating immune subpopulations abundances using gene expression data.
Maintained by Ajit Johnson Nirmal. Last updated 4 years ago.
cancerdeconvolutionimmunetranscriptomics
18.4 match 26 stars 4.11 score 8 scripts
hanjunwei-lab
SMDIC:Identification of Somatic Mutation-Driven Immune Cells
A computing tool is developed to automated identify somatic mutation-driven immune cells. The operation modes including: i) inferring the relative abundance matrix of tumor-infiltrating immune cells and integrating it with a particular gene mutation status, ii) detecting differential immune cells with respect to the gene mutation status and converting the abundance matrix of significant differential immune cell into two binary matrices (one for up-regulated and one for down-regulated), iii) identifying somatic mutation-driven immune cells by comparing the gene mutation status with each immune cell in the binary matrices across all samples, and iv) visualization of immune cell abundance of samples in different mutation status..
Maintained by Junwei Han. Last updated 5 months ago.
13.0 match 2 stars 4.00 score 5 scriptsbioc
EpiDISH:Epigenetic Dissection of Intra-Sample-Heterogeneity
EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of blood-tissue of any age, from birth to old-age, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.
Maintained by Shijie C. Zheng. Last updated 4 months ago.
dnamethylationmethylationarrayepigeneticsdifferentialmethylationimmunooncology
4.4 match 48 stars 10.28 score 166 scripts 4 dependents
ahgroup
DSAIRM:Dynamical Systems Approach to Immune Response Modeling
Simulation models (apps) of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.
Maintained by Andreas Handel. Last updated 8 months ago.
7.1 match 34 stars 6.19 score 23 scriptsbioc
ClustIRR:Clustering of immune receptor repertoires
ClustIRR analyzes repertoires of B- and T-cell receptors. It starts by identifying communities of immune receptors with similar specificities, based on the sequences of their complementarity-determining regions (CDRs). Next, it employs a Bayesian probabilistic models to quantify differential community occupancy (DCO) between repertoires, allowing the identification of expanding or contracting communities in response to e.g. infection or cancer treatment.
Maintained by Simo Kitanovski. Last updated 17 days ago.
clusteringimmunooncologysinglecellsoftwareclassificationb-cell-receptorbioinformaticsimmunoinformaticsimmunologyquantitative-methodsrep-seqrepertoire-analysist-cell-receptorcpp
7.1 match 2 stars 5.95 score 2 scriptsbioc
dandelionR:Single-cell Immune Repertoire Trajectory Analysis in R
dandelionR is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation. It provides the necessary functions to interface with scRepertoire and a custom implementation of an absorbing Markov chain for pseudotime inference, inspired by the Palantir Python package.
Maintained by Kelvin Tuong. Last updated 14 days ago.
softwareimmunooncologysinglecell
6.2 match 8 stars 5.81 score 7 scriptsbioc
spaSim:Spatial point data simulator for tissue images
A suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels.
Maintained by Yuzhou Feng. Last updated 5 months ago.
statisticalmethodspatialbiomedicalinformatics
6.9 match 2 stars 5.18 score 25 scripts
plangfelder
WGCNA:Weighted Correlation Network Analysis
Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.
Maintained by Peter Langfelder. Last updated 6 months ago.
3.6 match 54 stars 9.65 score 5.3k scripts 32 dependentsbioc
quantiseqr:Quantification of the Tumor Immune contexture from RNA-seq data
This package provides a streamlined workflow for the quanTIseq method, developed to perform the quantification of the Tumor Immune contexture from RNA-seq data. The quantification is performed against the TIL10 signature (dissecting the contributions of ten immune cell types), carefully crafted from a collection of human RNA-seq samples. The TIL10 signature has been extensively validated using simulated, flow cytometry, and immunohistochemistry data.
Maintained by Federico Marini. Last updated 3 months ago.
geneexpressionsoftwaretranscriptiontranscriptomicssequencingmicroarrayvisualizationannotationimmunooncologyfeatureextractionclassificationstatisticalmethodexperimenthubsoftwareflowcytometry
7.3 match 4.65 score 3 scripts 1 dependentsbioc
immApex:Tools for Adaptive Immune Receptor Sequence-Based Machine and Deep Learning
A set of tools to build tensorflow/keras3-based models in R from amino acid and nucleotide sequences focusing on adaptive immune receptors. The package includes pre-processing of sequences, unifying gene nomenclature usage, encoding sequences, and combining models. This package will serve as the basis of future immune receptor sequence functions/packages/models compatible with the scRepertoire ecosystem.
Maintained by Nick Borcherding. Last updated 19 days ago.
softwareimmunooncologysinglecellclassificationannotationsequencingmotifannotation
5.4 match 8 stars 5.92 score 3 scripts
rjknell
Biostatistics:Statistics Tutorials for Biologists
Tutorials for statistics, aimed at biological scientists. Subjects range from basic descriptive statistics through to complex linear modelling. The tutorials include text, videos, interactive coding exercises and multiple choice quizzes. The package also includes 19 datasets which are used in the tutorials.
Maintained by Rob Knell. Last updated 3 years ago.
7.1 match 4.54 score 5 scriptsbioc
scRepertoire:A toolkit for single-cell immune receptor profiling
scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, Omniscope, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R workflows.
Maintained by Nick Borcherding. Last updated 2 months ago.
softwareimmunooncologysinglecellclassificationannotationsequencingcpp
2.9 match 326 stars 10.49 score 240 scripts
openbiox
UCSCXenaShiny:Interactive Analysis of UCSC Xena Data
Provides functions and a Shiny application for downloading, analyzing and visualizing datasets from UCSC Xena (<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Maintained by Shixiang Wang. Last updated 4 months ago.
cancer-datasetshiny-appsucsc-xena
3.5 match 96 stars 8.54 score 35 scripts
mrc-ide
popim:POPulation IMmunity: Run a Demographic Model of Vaccine Exposure Over Time
Tools for setting up an age-structured population, applying vaccination activities to it, and tracking vaccine-induced immunity through time.
Maintained by Tini Garske. Last updated 2 months ago.
7.0 match 1 stars 4.15 score 4 scriptsbioc
SpatialDecon:Deconvolution of mixed cells from spatial and/or bulk gene expression data
Using spatial or bulk gene expression data, estimates abundance of mixed cell types within each observation. Based on "Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data", Danaher (2022). Designed for use with the NanoString GeoMx platform, but applicable to any gene expression data.
Maintained by Maddy Griswold. Last updated 5 months ago.
immunooncologyfeatureextractiongeneexpressiontranscriptomicsspatial
3.5 match 36 stars 7.40 score 58 scriptsbioc
mastR:Markers Automated Screening Tool in R
mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of group markers in various biological and medical applications, including cancer research and developmental biology.
Maintained by Jinjin Chen. Last updated 5 months ago.
softwaregeneexpressiontranscriptomicsdifferentialexpressionvisualization
5.1 match 4 stars 5.08 score 3 scripts
eonurk
cinaR:A Computational Pipeline for Bulk 'ATAC-Seq' Profiles
Differential analyses and Enrichment pipeline for bulk 'ATAC-seq' data analyses. This package combines different packages to have an ultimate package for both data analyses and visualization of 'ATAC-seq' data. Methods are described in 'Karakaslar et al.' (2021) <doi:10.1101/2021.03.05.434143>.
Maintained by Onur Karakaslar. Last updated 10 months ago.
atac-seqdifferential-analysisenrichment-analysisgene-sets
4.5 match 13 stars 5.52 score 51 scriptsbioc
cypress:Cell-Type-Specific Power Assessment
CYPRESS is a cell-type-specific power tool. This package aims to perform power analysis for the cell-type-specific data. It calculates FDR, FDC, and power, under various study design parameters, including but not limited to sample size, and effect size. It takes the input of a SummarizeExperimental(SE) object with observed mixture data (feature by sample matrix), and the cell-type mixture proportions (sample by cell-type matrix). It can solve the cell-type mixture proportions from the reference free panel from TOAST and conduct tests to identify cell-type-specific differential expression (csDE) genes.
Maintained by Shilin Yu. Last updated 5 months ago.
softwaregeneexpressiondataimportrnaseqsequencing
6.7 match 1 stars 3.70 score 2 scriptsbioc
xCell2:A Tool for Generic Cell Type Enrichment Analysis
xCell2 provides methods for cell type enrichment analysis using cell type signatures. It includes three main functions - 1. xCell2Train for training custom references objects from bulk or single-cell RNA-seq datasets. 2. xCell2Analysis for conducting the cell type enrichment analysis using the custom reference. 3. xCell2GetLineage for identifying dependencies between different cell types using ontology.
Maintained by Almog Angel. Last updated 18 hours ago.
geneexpressiontranscriptomicsmicroarrayrnaseqsinglecelldifferentialexpressionimmunooncologygenesetenrichment
4.0 match 6 stars 6.16 score 15 scriptsbioc
tidytof:Analyze High-dimensional Cytometry Data Using Tidy Data Principles
This package implements an interactive, scientific analysis pipeline for high-dimensional cytometry data built using tidy data principles. It is specifically designed to play well with both the tidyverse and Bioconductor software ecosystems, with functionality for reading/writing data files, data cleaning, preprocessing, clustering, visualization, modeling, and other quality-of-life functions. tidytof implements a "grammar" of high-dimensional cytometry data analysis.
Maintained by Timothy Keyes. Last updated 5 months ago.
singlecellflowcytometrybioinformaticscytometrydata-sciencesingle-celltidyversecpp
3.3 match 19 stars 7.26 score 35 scriptsbioc
signifinder:Collection and implementation of public transcriptional cancer signatures
signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures, based on gene expression values, and return single-sample scores. Currently, signifinder contains more than 60 distinct signatures collected from the literature, relating to multiple tumors and multiple cancer processes.
Maintained by Stefania Pirrotta. Last updated 2 months ago.
geneexpressiongenetargetimmunooncologybiomedicalinformaticsrnaseqmicroarrayreportwritingvisualizationsinglecellspatialgenesignaling
3.8 match 7 stars 6.40 score 15 scripts
cran
gss:General Smoothing Splines
A comprehensive package for structural multivariate function estimation using smoothing splines.
Maintained by Chong Gu. Last updated 5 months ago.
3.5 match 3 stars 6.40 score 137 dependents
stevencarlislewalker
mlmRev:Examples from Multilevel Modelling Software Review
Data and examples from a multilevel modelling software review as well as other well-known data sets from the multilevel modelling literature.
Maintained by Steve Walker. Last updated 5 years ago.
4.5 match 4.67 score 173 scripts
middleton-lab
abd:The Analysis of Biological Data
The abd package contains data sets and sample code for The Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009; Roberts & Company Publishers).
Maintained by Kevin M. Middleton. Last updated 11 months ago.
3.8 match 6 stars 5.53 score 182 scripts 1 dependents
niaid
HDStIM:High Dimensional Stimulation Immune Mapping ('HDStIM')
A method for identifying responses to experimental stimulation in mass or flow cytometry that uses high dimensional analysis of measured parameters and can be performed with an end-to-end unsupervised approach. In the context of in vitro stimulation assays where high-parameter cytometry was used to monitor intracellular response markers, using cell populations annotated either through automated clustering or manual gating for a combined set of stimulated and unstimulated samples, 'HDStIM' labels cells as responding or non-responding. The package also provides auxiliary functions to rank intracellular markers based on their contribution to identifying responses and generating diagnostic plots.
Maintained by Rohit Farmer. Last updated 1 years ago.
complexheatmapassaycytofcytometrycytometry-analysis-pipelineflowcytometrystimulation
4.7 match 3 stars 4.41 score 17 scriptsbioc
BulkSignalR:Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics
Inference of ligand-receptor (LR) interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics. BulkSignalR bases its inferences on the LRdb database included in our other package, SingleCellSignalR available from Bioconductor. It relies on a statistical model that is specific to bulk data sets. Different visualization and data summary functions are proposed to help navigating prediction results.
Maintained by Jean-Philippe Villemin. Last updated 3 months ago.
networkrnaseqsoftwareproteomicstranscriptomicsnetworkinferencespatial
3.8 match 5.22 score 15 scripts
epiverse-trace
finalsize:Calculate the Final Size of an Epidemic
Calculate the final size of a susceptible-infectious-recovered epidemic in a population with demographic variation in contact patterns and susceptibility to disease, as discussed in Miller (2012) <doi:10.1007/s11538-012-9749-6>.
Maintained by Rosalind Eggo. Last updated 1 months ago.
epidemic-modellingepidemiologyepiverseoutbreak-analysisrcppsdg-3cpp
2.4 match 11 stars 8.11 score 46 scripts
kaiaragaki
tidyestimate:A Tidy Implementation of 'ESTIMATE'
The 'ESTIMATE' package infers tumor purity from expression data as a function of immune and stromal infiltrate, but requires writing of intermediate files, is un-pipeable, and performs poorly when presented with modern datasets with current gene symbols. 'tidyestimate' a fast, tidy, modern reimagination of 'ESTIMATE' (2013) <doi:10.1038/ncomms3612>.
Maintained by Kai Aragaki. Last updated 2 years ago.
3.9 match 14 stars 4.85 score 4 scriptsbioc
SpaceMarkers:Spatial Interaction Markers
Spatial transcriptomic technologies have helped to resolve the connection between gene expression and the 2D orientation of tissues relative to each other. However, the limited single-cell resolution makes it difficult to highlight the most important molecular interactions in these tissues. SpaceMarkers, R/Bioconductor software, can help to find molecular interactions, by identifying genes associated with latent space interactions in spatial transcriptomics.
Maintained by Atul Deshpande. Last updated 5 months ago.
singlecellgeneexpressionsoftwarespatialtranscriptomics
3.0 match 5 stars 6.32 score 21 scriptsepiverse-trace
epidemics:Composable Epidemic Scenario Modelling
A library of compartmental epidemic models taken from the published literature, and classes to represent affected populations, public health response measures including non-pharmaceutical interventions on social contacts, non-pharmaceutical and pharmaceutical interventions that affect disease transmissibility, vaccination regimes, and disease seasonality, which can be combined to compose epidemic scenario models.
Maintained by Rosalind Eggo. Last updated 9 months ago.
decision-supportepidemic-modellingepidemic-simulationsepidemiologyepiverseinfectious-disease-dynamicsmodel-librarynon-pharmaceutical-interventionsrcpprcppeigenscenario-analysisvaccinationcpp
2.5 match 9 stars 7.48 score 59 scripts
zzawadz
DepthProc:Statistical Depth Functions for Multivariate Analysis
Data depth concept offers a variety of powerful and user friendly tools for robust exploration and inference for multivariate data. The offered techniques may be successfully used in cases of lack of our knowledge on parametric models generating data due to their nature. The package consist of among others implementations of several data depth techniques involving multivariate quantile-quantile plots, multivariate scatter estimators, multivariate Wilcoxon tests and robust regressions.
Maintained by Zygmunt Zawadzki. Last updated 3 years ago.
depth-functionsexploratory-data-analysisstatisticsopenblascppopenmp
3.4 match 6 stars 5.27 score 104 scripts 2 dependents
avi-kenny
vaccine:Statistical Tools for Immune Correlates Analysis of Vaccine Clinical Trial Data
Various semiparametric and nonparametric statistical tools for immune correlates analysis of vaccine clinical trial data. This includes calculation of summary statistics and estimation of risk, vaccine efficacy, controlled effects (controlled risk and controlled vaccine efficacy), and mediation effects (natural direct effect, natural indirect effect, proportion mediated). See Gilbert P, Fong Y, Kenny A, and Carone, M (2022) <doi:10.1093/biostatistics/kxac024> and Fay MP and Follmann DA (2023) <doi:10.48550/arXiv.2208.06465>.
Maintained by Avi Kenny. Last updated 23 days ago.
3.3 match 4 stars 5.42 score 11 scriptseonurk
cinaRgenesets:Ready-to-Use Curated Gene Sets for 'cinaR'
Immune related gene sets provided along with the 'cinaR' package.
Maintained by Onur Karakaslar. Last updated 4 years ago.
diceenrichmentenrichment-analysisgene-setsgenesetspbmcwikipathways
5.1 match 3 stars 3.35 score 15 scriptsmrc-ide
malariasimulation:An individual based model for malaria
Specifies the latest and greatest malaria model.
Maintained by Giovanni Charles. Last updated 28 days ago.
2.0 match 16 stars 8.17 score 146 scriptsbioc
LPE:Methods for analyzing microarray data using Local Pooled Error (LPE) method
This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library.
Maintained by Nitin Jain. Last updated 5 months ago.
microarraydifferentialexpression
3.4 match 4.58 score 21 scripts 1 dependentscran
Platypus:Single-Cell Immune Repertoire and Gene Expression Analysis
We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. This R version of 'Platypus' is part of the 'ePlatypus' ecosystem for computational analysis of immunogenomics data: Yermanos et al. (2021) <doi:10.1093/nargab/lqab023>, Cotet et al. (2023) <doi:10.1093/bioinformatics/btad553>.
Maintained by Alexander Yermanos. Last updated 5 months ago.
3.4 match 4.58 score 38 scriptsbioc
immunotation:Tools for working with diverse immune genes
MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have been reported, with significant differences in allele frequencies between human populations worldwide. Reproducible and consistent annotation of HLA alleles in large-scale bioinformatics workflows remains challenging, because the available reference databases and software tools often use different HLA naming schemes. The package immunotation provides tools for consistent annotation of HLA genes in typical immunoinformatics workflows such as for example the prediction of MHC-presented peptides in different human donors. Converter functions that provide mappings between different HLA naming schemes are based on the MHC restriction ontology (MRO). The package also provides automated access to HLA alleles frequencies in worldwide human reference populations stored in the Allele Frequency Net Database.
Maintained by Katharina Imkeller. Last updated 5 months ago.
softwareimmunooncologybiomedicalinformaticsgeneticsannotation
3.0 match 8 stars 4.90 score 3 scripts
reconhub
epitrix:Small Helpers and Tricks for Epidemics Analysis
A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymize data, and fitting discretized Gamma distributions.
Maintained by Thibaut Jombart. Last updated 2 years ago.
1.7 match 11 stars 8.58 score 231 scripts 5 dependents
tdhock
PeakSegJoint:Joint Peak Detection in Several ChIP-Seq Samples
Jointly segment several ChIP-seq samples to find the peaks which are the same and different across samples. The fast approximate maximum Poisson likelihood algorithm is described in "PeakSegJoint: fast supervised peak detection via joint segmentation of multiple count data samples" <doi:10.48550/arXiv.1506.01286> by TD Hocking and G Bourque.
Maintained by Toby Dylan Hocking. Last updated 3 months ago.
3.6 match 5 stars 4.00 score 66 scripts
airr-community
ogrdbstats:Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics
Multiple tools are now available for inferring the personalised germ line set from an adaptive immune receptor repertoire. Output from these tools is converted to a single format and supplemented with rich data such as usage and characterisation of 'novel' germ line alleles. This data can be particularly useful when considering the validity of novel inferences. Use of the analysis provided is described in <doi:10.3389/fimmu.2019.00435>.
Maintained by William Lees. Last updated 28 days ago.
3.3 match 1 stars 4.18 score 8 scripts
cobeylab
imprinting:Calculate Birth Year-Specific Probabilities of Immune Imprinting to Influenza
Reconstruct birth-year specific probabilities of immune imprinting to influenza A, using the methods of Gostic et al. (2016) <doi:10.1126/science.aag1322>. Plot, save, or export the calculated probabilities for use in your own research. By default, the package calculates subtype-specific imprinting probabilities, but with user-provided frequency data, it is possible to calculate probabilities for arbitrary kinds of primary exposure to influenza A, including primary vaccination and exposure to specific clades, strains, etc.
Maintained by Alex Byrnes. Last updated 2 years ago.
3.3 match 4.15 score 14 scripts
yaelsteu
ComICS:Computational Methods for Immune Cell-Type Subsets
Provided are Computational methods for Immune Cell-type Subsets, including:(1) DCQ (Digital Cell Quantifier) to infer global dynamic changes in immune cell quantities within a complex tissue; and (2) VoCAL (Variation of Cell-type Abundance Loci) a deconvolution-based method that utilizes transcriptome data to infer the quantities of immune-cell types, and then uses these quantitative traits to uncover the underlying DNA loci.
Maintained by Yael Steuerman. Last updated 7 years ago.
5.6 match 1 stars 2.36 score 19 scripts 2 dependents
augustinewigle
poth:Precision of Treatment Hierarchy (POTH)
Calculate POTH for treatment hierarchies from frequentist and Bayesian network meta-analysis. POTH quantifies the certainty in a treatment hierarchy. Subset POTH, POTH residuals, and cumulative POTH can also be calculated to improve interpretation of treatment hierarchies.
Maintained by Augustine Wigle. Last updated 5 months ago.
3.6 match 1 stars 3.65 score
statmanrobin
Lock5Data:Datasets for "Statistics: UnLocking the Power of Data"
Datasets for the third edition of "Statistics: Unlocking the Power of Data" by Lock^5 Includes version of datasets from earlier editions.
Maintained by Robin Lock. Last updated 4 years ago.
4.5 match 2.90 score 322 scriptsbioc
GmicR:Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
This package uses bayesian network learning to detect relationships between Gene Modules detected by WGCNA and immune cell signatures defined by xCell. It is a hypothesis generating tool.
Maintained by Richard Virgen-Slane. Last updated 5 months ago.
softwaresystemsbiologygraphandnetworknetworknetworkinferenceguiimmunooncologygeneexpressionqualitycontrolbayesianclustering
3.2 match 4.00 score 2 scripts
wtwt5237
DisHet:Estimate the Gene Expression Levels and Component Proportions of the Normal, Stroma (Immune) and Tumor Components of Bulk Tumor Samples
Model cell type heterogeneity of bulk renal cell carcinoma. The observed gene expression in bulk tumor sample is modeled by a log-normal distribution with the location parameter structured as a linear combination of the component-specific gene expressions.
Maintained by Tao Wang. Last updated 7 years ago.
7.8 match 1.30 score 3 scripts
canmod
macpan2:Fast and Flexible Compartmental Modelling
Fast and flexible compartmental modelling with Template Model Builder.
Maintained by Steve Walker. Last updated 2 days ago.
compartmental-modelsepidemiologyforecastingmixed-effectsmodel-fittingoptimizationsimulationsimulation-modelingcpp
1.1 match 4 stars 8.89 score 246 scripts 1 dependentsbioc
BiocFHIR:Illustration of FHIR ingestion and transformation using R
FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.
Maintained by Vincent Carey. Last updated 5 months ago.
infrastructuredataimportdatarepresentationfhir
1.6 match 4 stars 5.78 score 15 scriptscran
hbim:Hill/Bliss Independence Model for Combination Vaccines
Calculate expected relative risk and proportion protected assuming normally distributed log10 transformed antibody dose for a several component vaccine. Uses Hill models for each component which are combined under Bliss independence. See Saul and Fay, 2007 <DOI:10.1371/journal.pone.0000850>.
Maintained by Michael P. Fay. Last updated 2 years ago.
4.0 match 2.30 score
greifflab
immuneSIM:Tunable Simulation of B- And T-Cell Receptor Repertoires
Simulate full B-cell and T-cell receptor repertoires using an in silico recombination process that includes a wide variety of tunable parameters to introduce noise and biases. Additional post-simulation modification functions allow the user to implant motifs or codon biases as well as remodeling sequence similarity architecture. The output repertoires contain records of all relevant repertoire dimensions and can be analyzed using provided repertoire analysis functions. Preprint is available at bioRxiv (Weber et al., 2019 <doi:10.1101/759795>).
Maintained by Cédric R. Weber. Last updated 1 years ago.
1.7 match 37 stars 4.44 score 15 scriptseonurk
seAMLess:A Single Cell Transcriptomics Based Deconvolution Pipeline for Leukemia
Given a bulk transcriptomic (RNA-seq) sample of an Myeloid Leukemia patient calculates immune composition and drug resistance for different small-molecule inhibitors. Published in <https://www.nature.com/articles/s41698-024-00596-9>.
Maintained by E Onur Karakaslar. Last updated 3 months ago.
2.1 match 2 stars 3.60 score 7 scripts
tverbeke
SDaA:Sampling: Design and Analysis
Functions and Datasets from Lohr, S. (1999), Sampling: Design and Analysis, Duxbury.
Maintained by Tobias Verbeke. Last updated 3 years ago.
3.5 match 2.15 score 14 scripts
wanglabcsu
blit:Bioinformatics Library for Integrated Tools
An all-encompassing R toolkit designed to streamline the process of calling various bioinformatics software and then performing data analysis and visualization in R. With 'blit', users can easily integrate a wide array of bioinformatics command line tools into their workflows, leveraging the power of R for sophisticated data manipulation and graphical representation.
Maintained by Yun Peng. Last updated 2 days ago.
1.7 match 3 stars 4.38 score 3 scripts
andybega
spduration:Split-Population Duration (Cure) Regression
An implementation of split-population duration regression models. Unlike regular duration models, split-population duration models are mixture models that accommodate the presence of a sub-population that is not at risk for failure, e.g. cancer patients who have been cured by treatment. This package implements Weibull and Loglogistic forms for the duration component, and focuses on data with time-varying covariates. These models were originally formulated in Boag (1949) and Berkson and Gage (1952), and extended in Schmidt and Witte (1989).
Maintained by Andreas Beger. Last updated 1 years ago.
mixture-modelregressionsplit-populationsurvival-analysiscpp
1.2 match 4 stars 5.38 score 40 scripts
ssnn-airr
alakazam:Immunoglobulin Clonal Lineage and Diversity Analysis
Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>, Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Maintained by Susanna Marquez. Last updated 3 months ago.
0.5 match 9.09 score 424 scripts 7 dependentsbioc
SPIAT:Spatial Image Analysis of Tissues
SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.
Maintained by Yuzhou Feng. Last updated 17 hours ago.
biomedicalinformaticscellbiologyspatialclusteringdataimportimmunooncologyqualitycontrolsinglecellsoftwarevisualization
0.5 match 22 stars 8.59 score 69 scripts
kjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 11 months ago.
1.9 match 2.28 score 38 scripts
doehm
survivoR:Data from all Seasons of Survivor (US) TV Series in Tidy Format
Datasets detailing the results, castaways, and events of each season of Survivor for the US, Australia, South Africa, New Zealand, and the UK. This includes details on the cast, voting history, immunity and reward challenges, jury votes, boot order, advantage details, and episode ratings. Use this for analysis of trends and statistics of the game.
Maintained by Daniel Oehm. Last updated 2 days ago.
0.5 match 73 stars 7.08 score 94 scripts
bioc
scAnnotatR:Pretrained learning models for cell type prediction on single cell RNA-sequencing data
The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs.
Maintained by Johannes Griss. Last updated 5 months ago.
singlecelltranscriptomicsgeneexpressionsupportvectormachineclassificationsoftware
0.5 match 15 stars 6.73 score 20 scriptsbioc
COMPASS:Combinatorial Polyfunctionality Analysis of Single Cells
COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.
Maintained by Greg Finak. Last updated 5 months ago.
immunooncologyflowcytometrycpp
0.5 match 7 stars 6.51 score 42 scriptsbioc
CellBarcode:Cellular DNA Barcode Analysis toolkit
The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \code{CellBarcode} can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.
Maintained by Wenjie Sun. Last updated 12 days ago.
preprocessingqualitycontrolsequencingcrisprampliconamplicon-sequencingcellular-barcoderustcargo
0.5 match 1 stars 5.86 score 40 scriptsssnn-airr
scoper:Spectral Clustering-Based Method for Identifying B Cell Clones
Provides a computational framework for identification of B cell clones from Adaptive Immune Receptor Repertoire sequencing (AIRR-Seq) data. Three main functions are included (identicalClones, hierarchicalClones, and spectralClones) that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins) which share the same V gene, J gene and junction length. Nouri N and Kleinstein SH (2018) <doi: 10.1093/bioinformatics/bty235>. Nouri N and Kleinstein SH (2019) <doi: 10.1101/788620>. Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>.
Maintained by Susanna Marquez. Last updated 2 months ago.
0.5 match 5.43 score 89 scriptsbioc
VDJdive:Analysis Tools for 10X V(D)J Data
This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline. This includes reading the data into R, merging it with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots. It implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification.
Maintained by Kelly Street. Last updated 5 months ago.
softwareimmunooncologysinglecellannotationrnaseqtargetedresequencingcpp
0.5 match 7 stars 5.32 score 1 scriptsbioc
gcatest:Genotype Conditional Association TEST
GCAT is an association test for genome wide association studies that controls for population structure under a general class of trait models. This test conditions on the trait, which makes it immune to confounding by unmodeled environmental factors. Population structure is modeled via logistic factors, which are estimated using the `lfa` package.
Maintained by Alejandro Ochoa. Last updated 5 months ago.
snpdimensionreductionprincipalcomponentgenomewideassociation
0.5 match 5 stars 5.18 score 4 scriptsbioc
granulator:Rapid benchmarking of methods for *in silico* deconvolution of bulk RNA-seq data
granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles. The package provides a unified testing interface to rapidly run and benchmark multiple state-of-the-art deconvolution methods. Data for the deconvolution of peripheral blood mononuclear cells (PBMCs) into individual immune cell types is provided as well.
Maintained by Sabina Pfister. Last updated 5 months ago.
rnaseqgeneexpressiondifferentialexpressiontranscriptomicssinglecellstatisticalmethodregression
0.5 match 3 stars 4.48 score 7 scriptscran
AntibodyForests:Delineating Inter- And Intra-Antibody Repertoire Evolution
The generated wealth of immune repertoire sequencing data requires software to investigate and quantify inter- and intra-antibody repertoire evolution to uncover how B cells evolve during immune responses. Here, we present 'AntibodyForests', a software to investigate and quantify inter- and intra-antibody repertoire evolution.
Maintained by Daphne van Ginneken. Last updated 2 months ago.
0.8 match 2.70 score 2 scripts
computationalproteomics
proteoDeconv:Enabling Cell-Type Deconvolution of Proteomics Data
Tools for deconvoluting proteomics data to identify and quantify cell types (e.g., immune cell types) in complex biological samples.
Maintained by Måns Zamore. Last updated 2 days ago.
0.5 match 2 stars 3.85 score
richelbilderbeek
netmhc2pan:Interface to 'NetMHCIIpan'
The field of immunology benefits from software that can predict which peptide sequences trigger an immune response. 'NetMHCIIpan' is a such a tool: it predicts the binding strength of a short peptide to a Major Histocompatibility Complex class II (MHC-II) molecule. 'NetMHCIIpan' can be used from a web server at <https://services.healthtech.dtu.dk/services/NetMHCIIpan-3.2/> or from the command-line, using a local installation. This package allows to call 'NetMHCIIpan' from R.
Maintained by Richèl J.C. Bilderbeek. Last updated 8 months ago.
0.5 match 1 stars 3.70 score 8 scripts
login-
immunaut:Machine Learning Immunogenicity and Vaccine Response Analysis
Used for analyzing immune responses and predicting vaccine efficacy using machine learning and advanced data processing techniques. 'Immunaut' integrates both unsupervised and supervised learning methods, managing outliers and capturing immune response variability. It performs multiple rounds of predictive model testing to identify robust immunogenicity signatures that can predict vaccine responsiveness. The platform is designed to handle high-dimensional immune data, enabling researchers to uncover immune predictors and refine personalized vaccination strategies across diverse populations.
Maintained by Ivan Tomic. Last updated 5 months ago.
1.0 match 1.70 scorebioc
DeProViR:A Deep-Learning Framework Based on Pre-trained Sequence Embeddings for Predicting Host-Viral Protein-Protein Interactions
Emerging infectious diseases, exemplified by the zoonotic COVID-19 pandemic caused by SARS-CoV-2, are grave global threats. Understanding protein-protein interactions (PPIs) between host and viral proteins is essential for therapeutic targets and insights into pathogen replication and immune evasion. While experimental methods like yeast two-hybrid screening and mass spectrometry provide valuable insights, they are hindered by experimental noise and costs, yielding incomplete interaction maps. Computational models, notably DeProViR, predict PPIs from amino acid sequences, incorporating semantic information with GloVe embeddings. DeProViR employs a Siamese neural network, integrating convolutional and Bi-LSTM networks to enhance accuracy. It overcomes the limitations of feature engineering, offering an efficient means to predict host-virus interactions, which holds promise for antiviral therapies and advancing our understanding of infectious diseases.
Maintained by Matineh Rahmatbakhsh. Last updated 5 months ago.
proteomicssystemsbiologynetworkinferenceneuralnetworknetwork
0.5 match 1 stars 3.00 score 1 scripts
youyifong
copcor:Correlates of Protection and Correlates of Risk Functions
Correlates of protection (CoP) and correlates of risk (CoR) study the immune biomarkers associated with an infectious disease outcome, e.g. COVID or HIV-1 infection. This package contains shared functions for analyzing CoP and CoR, including bootstrapping procedures, competing risk estimation, and bootstrapping marginalized risks.
Maintained by Youyi Fong. Last updated 8 months ago.
0.5 match 2.90 score 16 scripts
matveevdaniil
RPatternJoin:String Similarity Joins for Hamming and Levenshtein Distances
This project is a tool for words edit similarity joins (a.k.a. all-pairs similarity search) under small (< 3) edit distance constraints. It works for Levenshtein/Hamming distances and words from any alphabet. The software was originally developed for joining amino-acid/nucleotide sequences from Adaptive Immune Repertoires, where the number of words is relatively large (10^5-10^6) and the average length of words is relatively small (10-100).
Maintained by Daniil Matveev. Last updated 5 months ago.
0.5 match 2.78 score 5 scripts 1 dependents
iembry
jab.adverse.reactions:Possible Adverse Events/Reactions from the Vaccinations/Experimental Gene Therapies
Provides data about the possible adverse events/reactions resulting from being injected with a vaccine/experimental gene therapy. Currently, this data set only includes information from six reference sources. Refer to the CITATION.cff file for the complete citations of the reference sources. For information about vaccination$/immunization$ hazards, visit <https://www.questionuniverse.com/rethink.html#vaccine>, <https://www.ecoccs.com/healing.html#vaccines>, <https://www.questionuniverse.com/rethink_current_crisis.html#cov_vaccin>, and <https://www.questionuniverse.com/vaccination.html>.
Maintained by Irucka Embry. Last updated 1 years ago.
0.5 match 2.70 scorecran
SeqFeatR:A Tool to Associate FASTA Sequences and Features
Provides user friendly methods for the identification of sequence patterns that are statistically significantly associated with a property of the sequence. For instance, SeqFeatR allows to identify viral immune escape mutations for hosts of given HLA types. The underlying statistical method is Fisher's exact test, with appropriate corrections for multiple testing, or Bayes. Patterns may be point mutations or n-tuple of mutations. SeqFeatR offers several ways to visualize the results of the statistical analyses, see Budeus (2016) <doi:10.1371/journal.pone.0146409>.
Maintained by Bettina Budeus. Last updated 6 years ago.
0.5 match 2.30 scorecran
eSIR:Extended State-Space SIR Models
An implementation of extended state-space SIR models developed by Song Lab at UM school of Public Health. There are several functions available by 1) including a time-varying transmission modifier, 2) adding a time-dependent quarantine compartment, 3) adding a time-dependent antibody-immunization compartment. Wang L. (2020) <doi:10.6339/JDS.202007_18(3).0003>.
Maintained by Michael Kleinsasser. Last updated 3 years ago.
0.5 match 1 stars 2.00 score
vavrycuk-zz
vaxpmx:Vaccines Pharmacometrics
Estimate vaccine efficacy (VE) using immunogenicity data. The inclusion of immunogenicity data in regression models can increase precision in VE. The methods are described in the publications "Elucidating vaccine efficacy using a correlate of protection, demographics, and logistic regression" and "Improving precision of vaccine efficacy evaluation using immune correlate data in time-to-event models" by Julie Dudasova, Zdenek Valenta, and Jeffrey R. Sachs (2024).
Maintained by Julie Dudasova (MSD). Last updated 4 months ago.
0.5 match 2.00 score
tianshilu
netie:Antigen T Cell Interaction Estimation
The Bayesian hierarchical model named antigen-T cell interaction estimation is to estimate the history of the immune pressure on the evolution of the tumor clones.The model is based on the estimation result from Andrew Roth (2014) <doi:10.1038/nmeth.2883>.
Maintained by Tianshi Lu. Last updated 3 years ago.
0.5 match 1.00 score
alexyermanos
VDJgermlines:Variable, Diversity and Joining Sequences from Various Species
Contains variable, diversity, and joining sequences and accompanying functions that enable both the extraction of and comparison between immune V-D-J genomic segments from a variety of species. Sources include IMGT from MP Lefranc (2009) <doi:10.1093/nar/gkn838> and Vgenerepertoire from publication DN Olivieri (2014) <doi:10.1007/s00251-014-0784-3>.
Maintained by Alexander Yermanos. Last updated 6 years ago.
0.5 match 1.00 score 3 scripts