Software Updates

Python

a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.

Julia

The Julia programming language is a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.

scvi-tools

(single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data.

tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.

IGV

(Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

PyRQA

a tool to conduct recurrence analysis in a massively parallel manner using the OpenCL framework.

DosageConvertor

DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.

CellRanger

Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.

NanoPack

A set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.

sniffles

Sniffles is a structural variation caller using third generation sequencing.

R-pkgs-Biogrids

contains common and requested R packages for BIOGRIDS. This title is dependent on R.

R

a free software environment for statistical computing and graphics.