Pinned Repositories
bridges2-examples
Different job examples running on Bridges-2
ml4docs
Machine Learning for Docs projects developed in collaboration with Prof. Raja Adal at Pitt.
neocortex-public
psync
Parallelized rsync-like clone
singularity-guppy-gpu
Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies’ basecalling algorithms.
singularity-homer
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
singularity-lazygit
Simple terminal UI for git commands
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.
slash2
SLASH2 file system
zfs-fuse
zfs-fuse maintanence clone
Pittsburgh Supercomputing Center's Repositories
pscedu/singularity-homer
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
pscedu/singularity-lazygit
Simple terminal UI for git commands
pscedu/asana
Helpful Asana scripts and Jupyter Notebooks
pscedu/singularity-fasttree
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
pscedu/singularity-gatk
The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data.
pscedu/workflow-examples
Just a collection of workflow examples for use on Bridges-2
pscedu/aibd-astrid-api
pscedu/aibd-bluetides-api
pscedu/singularity-abyss
ABySS is a de novo sequence assembler that is designed for very short reads
pscedu/singularity-anvio
Anvi’o is an open-source, community-driven analysis and visualization platform for microbial ‘omics.
pscedu/singularity-asciigenome
ASCIIGenome is a genome browser based on command line interface and designed for console terminals.
pscedu/singularity-asciinema
asciinema [as-kee-nuh-muh] is a free and open source solution for recording terminal sessions and sharing them on the web.
pscedu/singularity-aspera-connect
Aspera Connect helps you securely move file and folders of any size.
pscedu/singularity-augustus
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
pscedu/singularity-blat
BLAST-Like Alignment Tool.
pscedu/singularity-checkm
CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
pscedu/singularity-fastqc
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.
pscedu/singularity-ffmpeg
A complete, cross-platform solution to record, convert and stream audio and video.
pscedu/singularity-gent
This program computes the cross entropy for groups of sequences that have been assigned to groups on the basis of biochemical, physiological, or other biological property.
pscedu/singularity-hashdeep
md5deep is a set of programs to compute MD5, SHA-1, SHA-256, Tiger, or Whirlpool message digests on an arbitrary number of files.
pscedu/singularity-jq
jq is a lightweight and flexible command-line JSON processor.
pscedu/singularity-lowcharts
lowcharts is meant to be used in those scenarios where we have numerical data in text files that we want to display in the terminal to do a basic analysis.
pscedu/singularity-mc
GNU Midnight Commander is a visual file manager, licensed under GNU General Public License and therefore qualifies as Free Software.
pscedu/singularity-miller
Miller is a command-line tool for querying, shaping, and reformatting data files in various formats including CSV, TSV, JSON, and JSON lines.
pscedu/singularity-ncdu
ncdu is a disk utility for Unix systems
pscedu/singularity-rust
pscedu/singularity-tokei
Count your code, quickly.
pscedu/singularity-visidata
VisiData is an interactive multitool for tabular data.
pscedu/singularity-wordgrinder
A word processor which gets the hell out of your way and lets you get some work done.
pscedu/singularity-xxhash
xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit.