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ABCAllele-specific Binding from ChIP-Seq - a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments[ Lupien 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.[ ]
C3DA tool to predict 3D genomic interactions between cis-regulatory elements[ Lupien 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 ]
MEMOSMutation Enrichment of Motifs[ Lupien 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 ]
SMuRFSMuRF identifies significantly mutated genomic regions in a set of samples.[ Lupien 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 ]
VSEVariant Set Enrichment - an R package to identify disease-associated functional genomic regions[ Lupien 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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