- Computational doublet prediction for single cell RNA sequencing data — scds
Implements methods for computational doublet prediction: coexpression-based (cxds), binary-classification-based (bcds) and hybrid.
Associated publication:
scds: Computational Annotation of Doublets in Single Cell RNA Sequencing Data. AS Bais and D Kostka Bioinformatics, (accepted) 2019. ( doi ) - A database for cis-regulatory elements — creDB
Software package and database of cis-regulatory elements.
Associated publication:
Genome-wide Enhancer Maps Differ Significantly in Genomic Distribution, Evolution, and Function. ML Benton, SC Talipineni, D Kostka, JA Capra BMC Genomics 2019. ( doi ) - Lerning cell-cell similarities from scRNA-seq data — RAFSIL
Implements a two-step procedure using feature construction and random forest based similarity learning for single cell RNA sequencing data.
Associated publication:
Random forest based similarity learning for single cell RNA sequencing data. M Baranpouyan and D Kostka Bioinformatics, 34(13):i79-i88 2018. ( doi ) - Detection of lineage specific accelerated substitution rates — linACC
Exploits a hierarchy of nested evolutionary models to detect lineage specific acceleraton of substitution rates in different species/branches.
- Introduction to linACC (vignette)
- Download linACC R package
- Additional data/scripts for the analyses in the manuscript referenced below
Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages. D Kostka, AK Holloway, KS Pollard Molecular Biology and Evolution, 35(8):2034-2045 2018. ( doi ) - Lineage Dynamics for Epigenetics — lyne
Software package implementing continous time Markov models for epigenetic marks (like DNA methylation) on cell lineage trees.
Associated publication:
Modeling DNA methylation dynamics with approaches from phylogenetics. JA Capra and D Kostka Bioinformatics 2014, 30 (17), i408-i414. ( doi ) - Motif divergence between sequence pairs — motifDiverge
Software package implementing a statistical model for regulatory divergence based on transcription factor binding site motifs.
Associated publication:
motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences. D Kostka, T Friedrich, AK Holloway, KS Pollard Stat Interface 2015, 8(4): 463–476. ( doi )