Showing 42 of total 42 results (show query)
katilingban
ppitables:Lookup Tables to Generate Poverty Likelihoods and Rates using the Poverty Probability Index (PPI)
The Poverty Probability Index (PPI) is a poverty measurement tool for organizations and businesses with a mission to serve the poor. The PPI is statistically-sound, yet simple to use: the answers to 10 questions about a household's characteristics and asset ownership are scored to compute the likelihood that the household is living below the poverty line - or above by only a narrow margin. This package contains country-specific lookup data tables used as reference to determine the poverty likelihood of a household based on their score from the country-specific PPI questionnaire. These lookup tables have been extracted from documentation of the PPI found at <https://www.povertyindex.org> and managed by Innovations for Poverty Action <https://poverty-action.org/>.
Maintained by Ernest Guevarra. Last updated 4 days ago.
datapovertypoverty-likelihoodspoverty-probabilityppi
418.0 match 6 stars 6.43 score 89 scripts
ipd-tools
ipd:Inference on Predicted Data
Performs valid statistical inference on predicted data (IPD) using recent methods, where for a subset of the data, the outcomes have been predicted by an algorithm. Provides a wrapper function with specified defaults for the type of model and method to be used for estimation and inference. Further provides methods for tidying and summarizing results. Salerno et al., (2024) <doi:10.48550/arXiv.2410.09665>.
Maintained by Stephen Salerno. Last updated 2 months ago.
27.9 match 8 stars 6.13 score 5 scripts
adokter
bioRad:Biological Analysis and Visualization of Weather Radar Data
Extract, visualize and summarize aerial movements of birds and insects from weather radar data. See Dokter, A. M. et al. (2018) "bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028> for a software paper describing package and methodologies.
Maintained by Adriaan M. Dokter. Last updated 20 days ago.
aeroecologyenrameumetnet-operalifewatchmovement-ecologynexradoscibioradarweather-radarwsr-88d
15.2 match 29 stars 8.65 score 56 scripts
bioc
pathlinkR:Analyze and interpret RNA-Seq results
pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.
Maintained by Travis Blimkie. Last updated 3 months ago.
genesetenrichmentnetworkpathwaysreactomernaseqnetworkenrichmentbioinformaticsnetworkspathway-enrichment-analysisvisualization
10.5 match 26 stars 6.62 score 2 scripts
kasselhingee
scorematchingad:Score Matching Estimation by Automatic Differentiation
Hyvärinen's score matching (Hyvärinen, 2005) <https://jmlr.org/papers/v6/hyvarinen05a.html> is a useful estimation technique when the normalising constant for a probability distribution is difficult to compute. This package implements score matching estimators using automatic differentiation in the 'CppAD' library <https://github.com/coin-or/CppAD> and is designed for quickly implementing score matching estimators for new models. Also available is general robustification (Windham, 1995) <https://www.jstor.org/stable/2346159>. Already in the package are estimators for directional distributions (Mardia, Kent and Laha, 2016) <doi:10.48550/arXiv.1604.08470> and the flexible Polynomially-Tilted Pairwise Interaction model for compositional data. The latter estimators perform well when there are zeros in the compositions (Scealy and Wood, 2023) <doi:10.1080/01621459.2021.2016422>, even many zeros (Scealy, Hingee, Kent, and Wood, 2024) <doi:10.1007/s11222-024-10412-w>. A partial interface to CppAD's ADFun objects is also available.
Maintained by Kassel Liam Hingee. Last updated 2 months ago.
automatic-differentiationscore-matchingstatistical-inferencecpp
16.0 match 3.98 score 1 scriptsbioc
GeDi:Defining and visualizing the distances between different genesets
The package provides different distances measurements to calculate the difference between genesets. Based on these scores the genesets are clustered and visualized as graph. This is all presented in an interactive Shiny application for easy usage.
Maintained by Annekathrin Nedwed. Last updated 5 months ago.
guigenesetenrichmentsoftwaretranscriptionrnaseqvisualizationclusteringpathwaysreportwritinggokeggreactomeshinyapps
10.4 match 1 stars 5.52 score 22 scriptsbioc
wppi:Weighting protein-protein interactions
Protein-protein interaction data is essential for omics data analysis and modeling. Database knowledge is general, not specific for cell type, physiological condition or any other context determining which connections are functional and contribute to the signaling. Functional annotations such as Gene Ontology and Human Phenotype Ontology might help to evaluate the relevance of interactions. This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.
Maintained by Ana Galhoz. Last updated 5 months ago.
graphandnetworknetworkpathwayssoftwaregenesignalinggenetargetsystemsbiologytranscriptomicsannotationgene-ontologygene-prioritizationhuman-phenotype-ontologyomnipathppi-networksrandom-walk-with-restartquarto
11.0 match 1 stars 4.30 score 4 scriptsbioc
Path2PPI:Prediction of pathway-related protein-protein interaction networks
Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.
Maintained by Oliver Philipp. Last updated 5 months ago.
networkinferencesystemsbiologynetworkproteomicspathways
12.8 match 3.30 score 1 scriptsbioc
netresponse:Functional Network Analysis
Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling.
Maintained by Leo Lahti. Last updated 5 months ago.
cellbiologyclusteringgeneexpressiongeneticsnetworkgraphandnetworkdifferentialexpressionmicroarraynetworkinferencetranscription
7.1 match 3 stars 5.64 score 21 scripts
matthieustigler
tsDyn:Nonlinear Time Series Models with Regime Switching
Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Maintained by Matthieu Stigler. Last updated 5 months ago.
3.4 match 34 stars 10.56 score 684 scripts 3 dependentsbioc
R3CPET:3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results.
Maintained by Mohamed Nadhir Djekidel. Last updated 5 months ago.
networkinferencegenepredictionbayesiangraphandnetworknetworkgeneexpressionhicchia-petchromatin-interactiondirichlet-process-mixturestranscription-factocpp
6.3 match 4 stars 5.45 score 5 scriptsbioc
cisPath:Visualization and management of the protein-protein interaction networks.
cisPath is an R package that uses web browsers to visualize and manage protein-protein interaction networks.
Maintained by Likun Wang. Last updated 5 months ago.
8.8 match 3.30 score 9 scriptsbioc
magrene:Motif Analysis In Gene Regulatory Networks
magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan motifs. GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs. Motif frequencies can be analyzed in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks. Finally, users can calculate interaction similarity for gene pairs based on the Sorensen-Dice similarity index.
Maintained by Fabrício Almeida-Silva. Last updated 5 months ago.
softwaremotifdiscoverynetworkenrichmentsystemsbiologygraphandnetworkgene-regulatory-networkmotif-analysisnetwork-motifsnetwork-science
5.8 match 1 stars 4.00 score 2 scriptsbioc
HPiP:Host-Pathogen Interaction Prediction
HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data unavailability for HP-PPI network reconstructions. Moreover, establishing computational frameworks in that regard will reveal mechanistic insights into infectious diseases and suggest potential HP-PPI targets, thus narrowing down the range of possible candidates for subsequent wet-lab experimental validations.
Maintained by Matineh Rahmatbakhsh. Last updated 5 months ago.
proteomicssystemsbiologynetworkinferencestructuralpredictiongenepredictionnetwork
4.4 match 3 stars 4.95 score 6 scripts
ocbe-uio
DIscBIO:A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics
An open, multi-algorithmic pipeline for easy, fast and efficient analysis of cellular sub-populations and the molecular signatures that characterize them. The pipeline consists of four successive steps: data pre-processing, cellular clustering with pseudo-temporal ordering, defining differential expressed genes and biomarker identification. More details on Ghannoum et. al. (2021) <doi:10.3390/ijms22031399>. This package implements extensions of the work published by Ghannoum et. al. (2019) <doi:10.1101/700989>.
Maintained by Waldir Leoncio. Last updated 1 years ago.
biomarker-discoveryjupyter-notebookscrna-seqsingle-cell-analysistranscriptomicsopenjdk
5.0 match 12 stars 4.38 score 5 scriptsbioc
PPInfer:Inferring functionally related proteins using protein interaction networks
Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.
Maintained by Dongmin Jung. Last updated 5 months ago.
softwarestatisticalmethodnetworkgraphandnetworkgenesetenrichmentnetworkenrichmentpathways
4.5 match 4.48 score 4 scripts 1 dependents
saviviro
sstvars:Toolkit for Reduced Form and Structural Smooth Transition Vector Autoregressive Models
Penalized and non-penalized maximum likelihood estimation of smooth transition vector autoregressive models with various types of transition weight functions, conditional distributions, and identification methods. Constrained estimation with various types of constraints is available. Residual based model diagnostics, forecasting, simulations, and calculation of impulse response functions, generalized impulse response functions, and generalized forecast error variance decompositions. See Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>, Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>, Markku Lanne, Savi Virolainen (2025) <doi:10.48550/arXiv.2403.14216>, Savi Virolainen (2025) <doi:10.48550/arXiv.2404.19707>.
Maintained by Savi Virolainen. Last updated 17 days ago.
3.0 match 4 stars 6.36 score 41 scriptsbioc
OmnipathR:OmniPath web service client and more
A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).
Maintained by Denes Turei. Last updated 19 days ago.
graphandnetworknetworkpathwayssoftwarethirdpartyclientdataimportdatarepresentationgenesignalinggeneregulationsystemsbiologytranscriptomicssinglecellannotationkeggcomplexesenzyme-ptmnetworksnetworks-biologyomnipathproteinsquarto
1.9 match 126 stars 9.90 score 226 scripts 2 dependents
cran
crosstalkr:Analysis of Graph-Structured Data with a Focus on Protein-Protein Interaction Networks
Provides a general toolkit for drug target identification. We include functionality to reduce large graphs to subgraphs and prioritize nodes. In addition to being optimized for use with generic graphs, we also provides support to analyze protein-protein interactions networks from online repositories. For more details on core method, refer to Weaver et al. (2021) <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008755>.
Maintained by Davis Weaver. Last updated 10 months ago.
6.6 match 2.70 scorekatilingban
washdata:Urban Water and Sanitation Survey Dataset
Urban water and sanitation survey dataset collected by Water and Sanitation for the Urban Poor (WSUP) with technical support from Valid International. These citywide surveys have been collecting data allowing water and sanitation service levels across the entire city to be characterised, while also allowing more detailed data to be collected in areas of the city of particular interest. These surveys are intended to generate useful information for others working in the water and sanitation sector. Current release version includes datasets collected from a survey conducted in Dhaka, Bangladesh in March 2017. This survey in Dhaka is one of a series of surveys to be conducted by WSUP in various cities in which they operate including Accra, Ghana; Nakuru, Kenya; Antananarivo, Madagascar; Maputo, Mozambique; and, Lusaka, Zambia. This package will be updated once the surveys in other cities are completed and datasets have been made available.
Maintained by Ernest Guevarra. Last updated 11 months ago.
datasetsanitationurbanwashwater
3.8 match 4 stars 4.60 scorebioc
GSAR:Gene Set Analysis in R
Gene set analysis using specific alternative hypotheses. Tests for differential expression, scale and net correlation structure.
Maintained by Yasir Rahmatallah. Last updated 5 months ago.
softwarestatisticalmethoddifferentialexpression
3.9 match 4.38 score 7 scriptsbioc
vissE:Visualising Set Enrichment Analysis Results
This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches. Most enrichment analyses result in large lists of significant gene sets that are difficult to interpret. Tools in this package help build a similarity-based network of significant gene sets from a gene set enrichment analysis that can then be investigated for their biological function using text-mining approaches.
Maintained by Dharmesh D. Bhuva. Last updated 5 months ago.
softwaregeneexpressiongenesetenrichmentnetworkenrichmentnetworkbioinformatics
2.8 match 14 stars 5.90 score 19 scriptsbioc
CNORfeeder:Integration of CellNOptR to add missing links
This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links.
Maintained by Attila Gabor. Last updated 5 months ago.
cellbasedassayscellbiologyproteomicsnetworkinference
4.5 match 3.60 score 9 scriptsbioc
BioNAR:Biological Network Analysis in R
the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of diseases across the network and specific clusters pointing towards shared/common mechanisms.
Maintained by Anatoly Sorokin. Last updated 19 days ago.
softwaregraphandnetworknetwork
2.4 match 3 stars 5.90 score 35 scriptsbioc
pandaR:PANDA Algorithm
Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.
Maintained by Joseph N. Paulson. Last updated 5 months ago.
statisticalmethodgraphandnetworkmicroarraygeneregulationnetworkinferencegeneexpressiontranscriptionnetwork
3.5 match 3.30 score 8 scriptsbioc
BioNet:Routines for the functional analysis of biological networks
This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.
Maintained by Marcus Dittrich. Last updated 5 months ago.
microarraydataimportgraphandnetworknetworknetworkenrichmentgeneexpressiondifferentialexpression
1.8 match 6.14 score 114 scripts 2 dependents
dkahle
latte:Interface to 'LattE' and '4ti2'
Back-end connections to 'LattE' (<https://www.math.ucdavis.edu/~latte>) for counting lattice points and integration inside convex polytopes and '4ti2' (<http://www.4ti2.de/>) for algebraic, geometric, and combinatorial problems on linear spaces and front-end tools facilitating their use in the 'R' ecosystem.
Maintained by David Kahle. Last updated 2 years ago.
3.3 match 3 stars 3.18 score 1 scripts
keberwein
blscrapeR:An API Wrapper for the United States Bureau of Labor Statistics
Scrapes various data from <https://www.bls.gov/>. The Bureau of Labor Statistics is the statistical branch of the United States Department of Labor. The package has additional functions to help parse, analyze and visualize the data.
Maintained by Kris Eberwein. Last updated 1 years ago.
apiapi-wrapperblsbureau-of-labor-statisticsconsumer-price-indexcpiinflationinflation-calculatorlabor-statisticsunemployment
1.3 match 112 stars 7.66 score 270 scriptsbioc
Rcpi:Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery
A molecular informatics toolkit with an integration of bioinformatics and chemoinformatics tools for drug discovery.
Maintained by Nan Xiao. Last updated 5 months ago.
softwaredataimportdatarepresentationfeatureextractioncheminformaticsbiomedicalinformaticsproteomicsgosystemsbiologybioconductorbioinformaticsdrug-discoveryfeature-extractionfingerprintmolecular-descriptorsprotein-sequences
1.2 match 37 stars 7.81 score 29 scripts
nomahi
boutliers:Outlier detection and influence diagnostics for meta-analysis
A R package for implementing outlier detection and influence diagnostics for meta-analysis. Bootstrap distributions of the influence statistics are calculated, and the thresholds to determine outliers are clearly provided.
Maintained by Hisashi Noma. Last updated 3 years ago.
3.3 match 2.70 scorebioc
Rtpca:Thermal proximity co-aggregation with R
R package for performing thermal proximity co-aggregation analysis with thermal proteome profiling datasets to analyse protein complex assembly and (differential) protein-protein interactions across conditions.
Maintained by Nils Kurzawa. Last updated 5 months ago.
1.9 match 4.46 score 29 scripts
cogdisreslab
kinograte:Kinograte: Netwrok-based multi-omics Integration
Netwrok-based multi-omics integration using a prize-collecting Steiner forest (PCSF) algorithm.
Maintained by Khaled Alganem. Last updated 3 years ago.
4.0 match 1.70 score 2 scripts
hanjunwei-lab
ProgModule:Identification of Prognosis-Related Mutually Exclusive Modules
A novel tool to identify candidate driver modules for predicting the prognosis of patients by integrating exclusive coverage of mutations with clinical characteristics in cancer.
Maintained by Junwei Han. Last updated 3 months ago.
1.8 match 3.70 score 1 scriptsbioc
RITAN:Rapid Integration of Term Annotation and Network resources
Tools for comprehensive gene set enrichment and extraction of multi-resource high confidence subnetworks. RITAN facilitates bioinformatic tasks for enabling network biology research.
Maintained by Michael Zimmermann. Last updated 5 months ago.
qualitycontrolnetworknetworkenrichmentnetworkinferencegenesetenrichmentfunctionalgenomicsgraphandnetwork
1.1 match 5.40 score 9 scriptsbioc
geneplast:Evolutionary and plasticity analysis of orthologous groups
Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.
Maintained by Mauro Castro. Last updated 5 months ago.
geneticsgeneregulationsystemsbiology
1.2 match 4.13 score 17 scriptshanjunwei-lab
DTSEA:Drug Target Set Enrichment Analysis
It is a novel tool used to identify the candidate drugs against a particular disease based on the drug target set enrichment analysis. It assumes the most effective drugs are those with a closer affinity in the protein-protein interaction network to the specified disease. (See Gómez-Carballa et al. (2022) <doi: 10.1016/j.envres.2022.112890> and Feng et al. (2022) <doi: 10.7150/ijms.67815> for disease expression profiles; see Wishart et al. (2018) <doi: 10.1093/nar/gkx1037> and Gaulton et al. (2017) <doi: 10.1093/nar/gkw1074> for drug target information; see Kanehisa et al. (2021) <doi: 10.1093/nar/gkaa970> for the details of KEGG database.)
Maintained by Junwei Han. Last updated 2 years ago.
1.1 match 4.32 score 42 scriptsbioc
BioNERO:Biological Network Reconstruction Omnibus
BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. BioNERO can be used to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) from gene expression data. Additionally, it can be used to explore topological properties of protein-protein interaction (PPI) networks. GCN inference relies on the popular WGCNA algorithm. GRN inference is based on the "wisdom of the crowds" principle, which consists in inferring GRNs with multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average rank for each interaction pair. As all steps of network analyses are included in this package, BioNERO makes users avoid having to learn the syntaxes of several packages and how to communicate between them. Finally, users can also identify consensus modules across independent expression sets and calculate intra and interspecies module preservation statistics between different networks.
Maintained by Fabricio Almeida-Silva. Last updated 5 months ago.
softwaregeneexpressiongeneregulationsystemsbiologygraphandnetworkpreprocessingnetworknetworkinference
0.5 match 27 stars 7.78 score 50 scripts 1 dependents
dosorio
SCORPION:Single Cell Oriented Reconstruction of PANDA Individual Optimized Networks
Constructs gene regulatory networks from single-cell gene expression data using the PANDA (Passing Attributes between Networks for Data Assimilation) algorithm.
Maintained by Daniel Osorio. Last updated 10 months ago.
3.4 match 1.00 score 8 scriptsbioc
DeepPINCS:Protein Interactions and Networks with Compounds based on Sequences using Deep Learning
The identification of novel compound-protein interaction (CPI) is important in drug discovery. Revealing unknown compound-protein interactions is useful to design a new drug for a target protein by screening candidate compounds. The accurate CPI prediction assists in effective drug discovery process. To identify potential CPI effectively, prediction methods based on machine learning and deep learning have been developed. Data for sequences are provided as discrete symbolic data. In the data, compounds are represented as SMILES (simplified molecular-input line-entry system) strings and proteins are sequences in which the characters are amino acids. The outcome is defined as a variable that indicates how strong two molecules interact with each other or whether there is an interaction between them. In this package, a deep-learning based model that takes only sequence information of both compounds and proteins as input and the outcome as output is used to predict CPI. The model is implemented by using compound and protein encoders with useful features. The CPI model also supports other modeling tasks, including protein-protein interaction (PPI), chemical-chemical interaction (CCI), or single compounds and proteins. Although the model is designed for proteins, DNA and RNA can be used if they are represented as sequences.
Maintained by Dongmin Jung. Last updated 5 months ago.
softwarenetworkgraphandnetworkneuralnetworkopenjdk
0.5 match 4.78 score 4 scripts 2 dependents
huerqiang
prioGene:Candidate Gene Prioritization for Non-Communicable Diseases Based on Functional Information
In gene sequencing methods, the topological features of protein-protein interaction (PPI) networks are often used, such as ToppNet <https://toppgene.cchmc.org>. In this study, a candidate gene prioritization method was proposed for non-communicable diseases considering disease risks transferred between genes in weighted disease PPI networks with weights for nodes and edges based on functional information.
Maintained by Erqiang Hu. Last updated 5 years ago.
graphandnetworkfunctionalgenomicsgeneticsnetwork
0.8 match 3.00 score 10 scriptshanjunwei-lab
ssMutPA:Single-Sample Mutation-Based Pathway Analysis
A systematic bioinformatics tool to perform single-sample mutation-based pathway analysis by integrating somatic mutation data with the Protein-Protein Interaction (PPI) network. In this method, we use local and global weighted strategies to evaluate the effects of network genes from mutations according to the network topology and then calculate the mutation-based pathway enrichment score (ssMutPES) to reflect the accumulated effect of mutations of each pathway. Subsequently, the ssMutPES profiles are used for unsupervised spectral clustering to identify cancer subtypes.
Maintained by Junwei Han. Last updated 5 months ago.
0.5 match 4.00 score 9 scripts