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BEHSTAssociating functional enriched Gene Ontology terms to input genomic regions[ Hoffman Lab ]

BamgineerSimulation of user-defined, allele-specific copy number events into bam files.[ Pugh Lab ]

Bi-LSTM 1 (LDCT Report NLP Model)Best-performing in-house NLP model for parsing LDCT radiology reports.[ Liu G. Lab ]

CREAMClustering of Genomic Regions Analysis Method[ Haibe-Kains Lab ]

ConsensusCruncherSuppresses errors in next-generation sequencing data by using unique molecular identifiers[ Pugh Lab ]

CytoscapeNetwork Data Integration, Analysis, and Visualization in a Box[ Bader Lab ]

FrustrationStructural genomics method to priortize missense mutations[ Kumar Lab ]

GENmaticGENmatic is a consistent R interface to do genetic QC and Analysis.[ Xu Lab ]

GenomedataEfficient storage of multiple tracks of numeric data anchored to a genome[ Hoffman Lab ]

HeatITupFind and annotate internal tandem duplications within sequences.[ Schwartz Lab ]

HotCommicsMutation clustering approach to identify putative cancer driver genes[ Kumar Lab ]

LDCT NERAn open source, high-performance information extraction NER model for LDCT reports.[ Xu Lab ]

PeaKODiscoversing motifs in ChIP-seq datasets with knockout controls[ Hoffman Lab ]

PharmacoGxAnalysis of large-scale pharmacogenomic datasets[ Haibe-Kains Lab ]

PymRMReParallelized minimum Redundancy Maximum Relevance ensemble feature selection[ Haibe-Kains Lab ]

RLOBICOR implementation of logic optimization for binary input to continuous output[ Haibe-Kains Lab ]

RadioGxAnalysis of Large-Scale Radio-Genomic Data[ Haibe-Kains Lab ]

SIGNSimilarity Identification in Gene Expression[ Haibe-Kains Lab ]

SVFXSupervised machine learning method to priortize SVs[ Kumar Lab ]

SegtoolsVisualizing and analyzing genomic segmentations[ Hoffman Lab ]

SegwaySegmentation and genome annotation[ Hoffman Lab ]

TooManyCellsA suite of algorithms and visualizations focusing on the relationships between cell clades.[ Schwartz Lab ]

ToxicoGxAnalysis of Large-Scale Toxico-Genomic Data[ Haibe-Kains Lab ]

Umap and BismapQuantifying mappability of the genome and methylome[ Hoffman Lab ]

VirchipPredicting transcription factor binding by learning from the transcriptome[ Hoffman Lab ]

VisCapFor inference and visualization of germline copy number variants (CNVs) from targeted NGS data.[ Pugh Lab ]

VisCapCancerTool for calling tumour-specific somatic copy number alterations from targeted sequencing data[ Pugh Lab ]

XevaAnalysis of patient-derived xenograft (PDX) data[ Haibe-Kains Lab ]

diversityFind the diversity of a collection of entities.[ Schwartz Lab ]

fastaFasta parser for various string types.[ Schwartz Lab ]

find-clumpinessFind the clumpiness of labels in tree structure.[ Schwartz Lab ]

inteGREATinteGREAT is an algorithm for integrating multiple data sources.[ Schwartz Lab ]

mRMReParallelized Minimum Redundancy, Maximum Relevance (mRMR) Ensemble Feature Selection[ Haibe-Kains Lab ]

pdfcommentspdfcomments extracts comments from a PDF and puts them in a text file.[ Hoffman Lab ]

ploterificPlot tabular data from the command line.[ Schwartz Lab ]

remssremss is a package for TNM stage is important in treatment decision-making and outcome predicting.[ Xu Lab ]

xlinkAnalyze X-linked genetic association for phenotype over all of the potential biological processes[ Xu Lab ]

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