Site identification in high-throughput RNA-protein interaction data
Pathway-based visualization of cross-platform microarray datasets
‘Location, Location, Location’: a spatial approach for rare variant analysis and an application to a study on non-syndromic cleft lip with or without cleft palate
Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches
Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes
SCALCE: boosting sequence compression algorithms using locally consistent encoding
Predicting pseudoknotted structures across two RNA sequences
Predicting protein residue-residue contacts using deep networks and boosting
Gene set analysis for self-contained tests: complex null and specific alternative hypotheses
An unbiased evaluation of gene prioritization tools
Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks
Robust design of microbial strains
Global network alignment using multiscale spectral signatures
Network-based inference from complex proteomic mixtures using SNIPE
Multinomial modeling and an evaluation of common data-mining algorithms for identifying signals of disproportionate reporting in pharmacovigilance databases
HiCNorm: removing biases in Hi-C data via Poisson regression
Advanced Complex Trait Analysis
FeatureStack: Perl module for comparative visualization of gene features
Creating reusable tools from scripts: the Galaxy Tool Factory
KGBassembler: a karyotype-based genome assembler for Brassicaceae species
Adding unaligned sequences into an existing alignment using MAFFT and LAST
ncPRO-seq: a tool for annotation and profiling of ncRNAs in sRNA-seq data
CD-HIT: accelerated for clustering the next-generation sequencing data
fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays
MesoRD 1.0: Stochastic reaction-diffusion simulations in the microscopic limit
SemMedDB: a PubMed-scale repository of biomedical semantic predications
KASpOD—a web service for highly specific and explorative oligonucleotide design
InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data
miR-EdiTar: a database of predicted A-to-I edited miRNA target sites