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.

scvi-tools

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

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.

Google Cloud SDK

tools and libraries for interacting with Google Cloud products and services.

emacs

An extensible, customizable, free/libre text editor.

R-pkgs-Biogrids

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

MAFFT

a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).

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

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.

DosageConvertor

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

Cell Ranger

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

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.