Software

More repositories on GitHub.

Command-line tools

Deep learning

🧐 duvidNN

Deep learning with uncertainty for general purpose, chemistry, and taxonomic tasks.

https://github.com/scbirlab/duvidnn

🚄 lchemme

Training and applying large chemistry models for embeddings.

https://github.com/scbirlab/lchemme

🍐 yunta

Predicting protein-protein interactions and structures from multiple sequence alignments.

https://github.com/scbirlab/yunta

Cheminformatics

⬢⬢⬢ schemist

Organizing and processing arbitrarily large tables of chemical structures.

https://github.com/scbirlab/schemist

Functional genomics and molecular biology

🌱 crispio

Designing CRISPRi experiments in bacteria.

https://github.com/scbirlab/crispio

⛓️ ogilo

Automate construction of oligo library sequences for oligo array synthesis.

https://github.com/scbirlab/ogilo

🔴🟢🔵⚫️ monte barcode

Generate sets of random DNA sequences optimized for use in high-throughput sequencing.

https://github.com/scbirlab/monte-barcode

🧬 streq

Python utilities for working with nucleotide sequences.

https://github.com/scbirlab/streq

Miscellaneous

🧠 nemony

Deterministically encode arbitrary text such as nucleotide sequences as mnemonic adjective-noun pairs.

https://github.com/scbirlab/nemony

Nextflow pipelines

🧮 scbirlab/nf-crispriseq

Calculate fitness from massive competition experiments using CRISPRi-seq.

https://github.com/scbirlab/nf-crispriseq

🧬 scbirlab/nf-ont-call-variants

Call variants from Nanopore FASTQ files from bacterial clones relative to a wildtype control.

https://github.com/scbirlab/nf-ont-call-variants

🧬 scbirlab/nf-ggi

Computationally screen for gene-gene interactions within an organism or between organisms.

https://github.com/scbirlab/nf-ggi