4-class classifier of metagenome contigs using machine learning and assembly graphs
Integrating gene expression and DNA methylation datasets for disjoint sample sets.
Selecting minimizers based on minimum decycling set.
Long-read mapping using syncmers.
CT-FOCS - A database of cell type-specific enhancer-promoter links
Dataset adaptive minimizer order generator for binning applications
3-class classification of metagenome assemblies
Accurate module discovery using gene activities and a network
Multi Omic clustering by Non-Exhaustive Types
Complete plasmid assembly in metagenomes
Empirically correcting the functional significance of GO terms in modules
PlasClass - Plasmid sequence classifier
NEMO: Neighborhood based multi-omics clustering algorithm
PROMO - a tool for analysis and visualization of large multi-omic and clinical datasets.
EXPANDER - A one stop-shop platform for all analysis steps of gene expression data.
Faucet: streaming de novo assembly graph construction
FOCS: A database of human and mouse enhancer-promoter links
Adeptus - A database and tools for multi-disease analysis.
Recycler - detecting plasmids from de novo assembly graphs
DOCKS - A software for designing compact universal k-mers hitting set.
RichMind - Analysis of enrichment within neuroimaging findings
Motif finding from high-throughput SELEX
ElemeNT - Tool for detection of core promoter elements.
BARCODE - A fast lossless read compression tool based on Bloom filters.
RAP - A software for inferring binding site motifs from protein binding microarrays.
HiDe - A software for inferring highways of horizontal gene transfer.
ShortCAKE - Designing a shortest DNA sequence that covers all k-mers, exploiting reverse complementarity.
ModEnt - A tool that reconstructs gene regulatory networks from high throughput experimental data.
AMADEUS - Platform for de novo motif discovery in DNA sequences.
ALLEGRO - Software for simultaneous discovery of cis-regulatory motifs and their associated expression profiles.
Morph - A webtool and software for ranking candidate genes in pathways.
STACK - Analyzing statistical associations among cancer karyotypes.
FAME - A tool for Functional Assignment to MicroRNAs via Enrichment
TORQUE - Topology-free querying of protein interaction networks.
MetaReg - A tool for modeling of biological systems
HYDEN - A software for designing degenerate primers.
SPIKE - (previously SHARP). Signaling pathways integrated knowledge engine.
MATISSE - A tool for joint analysis of interaction networks and gene expression data.
GEVALT - An integrated software for genotype analysis.
PSAT - Evaluating the significance of association scores in whole-genome cohorts with stratification.
Cofactors - Linking transcription factors and chromatin modifiers.
RAT - A software for rapid association tests.
Cisprof - Evolutionary mechanisms underlying conservation and evolvability in regulatory networks.
PREVO - An analysis of the network of selection forces in the evolution of yeast cis-regulation
SIMBA - System level analysis of yeast by exploring of large-scale biological compendia.
SAMBA - Module discovery in highly diverse genome-wide datasets using biclustering.
GREAL - software for the graph realization Problem.
PRIMA - A program for finding transcription factors whose binding sites are enriched in a given set of promoters.
PIVOT - Java-based protein interactions visualization tool.
