Pittsburgh Supercomputing Center

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197 repositories

basic-plotting
Public
Plotting for Data Scientists
Jupyter Notebook
•0•0•0•0•Updated Dec 9, 2025Dec 9, 2025
psc-wpdocs
Public
WeDocs repo for documentation on PSC.edu
4•1•1•1•Updated Oct 7, 2025Oct 7, 2025
pegasus-psc
Public
example workflow for running on neocortex, using Cerebras training examples
Python
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Apache License 2.0
•1•0•0•0•Updated Oct 7, 2025Oct 7, 2025
singularity-report
Public
Just a list of Singularity definition files maintained by the Biomed Applications Group
singularity biomedical-informatics containerization biomedical-data-science
Python
•0•0•0•0•Updated Sep 12, 2025Sep 12, 2025
nf-configs
Public
Config files used to define parameters specific to compute environments at different Institutions
Nextflow
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MIT License
•339•0•0•0•Updated Sep 2, 2025Sep 2, 2025
singularity-dust
Public
du + rust = dust. Like du but more intuitive.
utilities singularity
Shell
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Apache License 2.0
•0•0•1•0•Updated Aug 19, 2025Aug 19, 2025
singularity-vcf2maf
Public
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
bioinformatics singularity
Shell
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Apache License 2.0
•0•1•1•0•Updated Aug 19, 2025Aug 19, 2025
singularity-papis
Public
Powerful and highly extensible command-line based document and bibliography manager.
singularity
Lua
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Apache License 2.0
•0•0•1•0•Updated Aug 19, 2025Aug 19, 2025
singularity-pandiff
Public
Prose diffs for any document format supported by Pandoc
Shell
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Apache License 2.0
•0•0•0•0•Updated Aug 19, 2025Aug 19, 2025
singularity-nanoplot
Public
Plotting scripts for long read sequencing data
Shell
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Apache License 2.0
•0•0•1•0•Updated Aug 19, 2025Aug 19, 2025
singularity-hyperfine
Public
A command-line benchmarking tool.
utilities singularity
Shell
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Apache License 2.0
•0•0•2•0•Updated Aug 19, 2025Aug 19, 2025
singularity-btop
Public
A monitor of resources
utilities singularity
Shell
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Apache License 2.0
•0•0•1•0•Updated Aug 19, 2025Aug 19, 2025
singularity-anvio
Public
Anvi’o is an open-source, community-driven analysis and visualization platform for microbial ‘omics.
bioinformatics singularity
Lua
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Apache License 2.0
•0•0•1•0•Updated Aug 19, 2025Aug 19, 2025
singularity-wordgrinder
Public
A word processor which gets the hell out of your way and lets you get some work done.
utilities singularity
Shell
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Apache License 2.0
•0•0•1•0•Updated Aug 13, 2025Aug 13, 2025
singularity-visidata
Public
VisiData is an interactive multitool for tabular data.
utilities singularity
Shell
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Apache License 2.0
•1•0•0•0•Updated Aug 13, 2025Aug 13, 2025
singularity-viennarna
Public
The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
bioinformatics singularity
Shell
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Apache License 2.0
•0•0•2•0•Updated Aug 13, 2025Aug 13, 2025
singularity-trimmomatic
Public
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data
bioinformatics singularity
Lua
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Apache License 2.0
•1•0•0•0•Updated Aug 13, 2025Aug 13, 2025
singularity-stride
Public
Protein secondary structure assignment
singularity
Shell
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Apache License 2.0
•0•0•0•0•Updated Aug 13, 2025Aug 13, 2025
singularity-star-fusion
Public
STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT).
bioinformatics singularity
Lua
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Apache License 2.0
•0•0•1•0•Updated Aug 13, 2025Aug 13, 2025
singularity-star
Public
Spliced Transcripts Alignment to a Reference.
bioinformatics singularity
Lua
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Apache License 2.0
•0•0•1•0•Updated Aug 13, 2025Aug 13, 2025
singularity-sra-toolkit
Public
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.
bioinformatics singularity
Shell
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Apache License 2.0
•0•0•2•0•Updated Aug 13, 2025Aug 13, 2025
singularity-spades
Public
SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.
bioinformatics singularity
Shell
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Apache License 2.0
•0•0•0•0•Updated Aug 13, 2025Aug 13, 2025
singularity-shellcheck
Public
ShellCheck, a static analysis tool for shell scripts
utilities singularity
Shell
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Apache License 2.0
•1•0•1•0•Updated Aug 13, 2025Aug 13, 2025
singularity-samtools
Public
Samtools is a suite of programs for interacting with high-throughput sequencing data.
bioinformatics singularity
Shell
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Apache License 2.0
•0•0•1•0•Updated Aug 13, 2025Aug 13, 2025
singularity-salmon
Public
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
bioinformatics singularity
Shell
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Apache License 2.0
•0•0•1•0•Updated Aug 13, 2025Aug 13, 2025
singularity-rust
Public
Rust is blazingly fast and memory-efficient
singularity
Shell
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Apache License 2.0
•0•0•0•0•Updated Aug 13, 2025Aug 13, 2025
singularity-rnaview
Public
RNAView identifies base pairs that are formed in nucleic acid structures and classifies them according to the system of Leontis and Westhof
singularity
Shell
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Apache License 2.0
•0•0•0•0•Updated Aug 13, 2025Aug 13, 2025
singularity-rich-cli
Public
Build amazing TUIs (Text User Interfaces) with this innovative Python framework.
utilities singularity
Lua
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Apache License 2.0
•0•0•0•0•Updated Aug 13, 2025Aug 13, 2025
singularity-rclone
Public
Rclone is a command line program to manage files on cloud storage. It is a feature rich alternative to cloud vendors' web storage interfaces.
utilities singularity
Shell
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Apache License 2.0
•0•3•1•0•Updated Aug 13, 2025Aug 13, 2025
singularity-raxml
Public
RAxML - Randomized Axelerated Maximum Likelihood.
bioinformatics singularity
Lua
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Apache License 2.0
•0•0•0•0•Updated Aug 13, 2025Aug 13, 2025