kallisto
Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets)
Software (C++)
https://pachterlab.github.io/kallisto/
Sailfish
Estimation of isoform abundances...
Network analysis is any structured technique used to mathematically analyze a circuit (a “network” of interconnected components). The Network analysis provides the ability to quantify associations between individuals, which...
Meaningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurate calling of SNPs and genotypes. Recently developed statistical methods both improve and...
github.com - Binaries of ngs-bits are available via Bioconda. Alternatively, ngs-bits can be built from sources:
Binaries for Linux/macOS
From sources for Linux/macOS
From sources for Windows
biokit.readthedocs.io - BioKit is a set of tools dedicated to bioinformatics, data visualisation (biokit.viz), access to online biological data (e.g. UniProt, NCBI thanks to bioservices). It also contains more advanced tools related to data analysis...
github.com - HiCdat: a fast and easy-to-use Hi-C data analysis tool
HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes,...
https://fuma.ctglab.nl/ - FUMA is a platform that can be used to annotate, prioritize, visualize and interpret GWAS results. The SNP2GENE function takes GWAS summary statistics as an input, and provides extensive functional annotation for all SNPs in genomic...