Pittsburgh Supercomputing Center's repositories
singularity-rclone
Rclone is a command line program to manage files on cloud storage. It is a feature rich alternative to cloud vendors' web storage interfaces.
singularity-aws-cli
The AWS Command Line Interface (CLI) is a unified tool to manage your AWS services.
eclipdemux
demultiplex utility for eclip raw fastq files (process eclip barcodes and ramdomers)
matconvnet
MatConvNet: CNNs for MATLAB
nextflow-examples
Just a set of netflow example scripts
OpenLongTailRecognition-OLTR
Pytorch implementation for "Large-Scale Long-Tailed Recognition in an Open World" (CVPR 2019 ORAL)
singularity-bedtools
A powerful toolset for genome arithmetic.
singularity-bioformats2raw
Bio-Formats image file format to raw format converter.
singularity-bpytop
Resource monitor that shows usage and stats for processor, memory, disks, network and processes.
singularity-braker2
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.
singularity-bsmap
BSMAP is a short reads mapping software for bisulfite sequencing reads.
singularity-bwa
BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome).
singularity-fastq-tools
Small utilities for working with fastq sequence files.
singularity-funannotate
Eukaryotic Genome Annotation Pipeline
singularity-glances
Glances is a cross-platform system monitoring tool written in Python.
singularity-hmmer
HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
singularity-hyperfine
A command-line benchmarking tool.
singularity-kakoune
Kakoune is a code editor heavily inspired by Vim.
singularity-libtiff-tools
A small collection of programs for converting non-TIFF format images to TIFF and for manipulating and interogating the contents of TIFF images.
singularity-meme-suite
The MEME Suite allows you to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.
singularity-octave
GNU Octave is software featuring a high-level programming language, primarily intended for numerical computations
singularity-pandiff
Prose diffs for any document format supported by Pandoc
singularity-rich-cli
Build amazing TUIs (Text User Interfaces) with this innovative Python framework.
singularity-spades
SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.
singularity-star
Spliced Transcripts Alignment to a Reference.
singularity-star-fusion
STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT).