tools

This is a collection of many of the tools, libraries, and pipelines I've written over the years organized by the context I built them in.

Tools

CRISPR Screening Platform

• sgcount
  • Mapping sgRNA counts for CRISPRi/a screens.
• casmap
  • Mapping sgRNA counts for CAS12 6-plex CRISPR screens.
• crispr_screen
  • Perform differential abundance testing and sgrna -> guide aggregation for CRISPR screens.
• screenviz
  • Visualize and interact with CRISPR screen results in the browser.

Single-Cell Sequencing

• geomux
  • Assign cells to features using a hypergeometric based test.
• adpbulk
  • Perform pseudobulking of single-cell sequencing data for differential expression testing.
• cshift
  • Perform differential representation testing for groups and clusters in single-cell sequencing data.
• pypage
  • Conditional mutual information based pathway analysis (GSEA alternative)
• IDEA
  • Integrated Differential Expression and Annotation. Visualizes the bipartite graph of gene sets and overlapping differentially expressed genes in an interactive force-directed graph.

Bioinformatics CLI Tools

• gia

  • A command-line genome interval arithmetic toolkit written in rust. Takes advantage of bedrs for powerful trait based interval operations.

• ggetrs

  • A rust implementation of gget that takes advantage of powerful rust async and execution times. Provides a single interface to perform queries on multiple bioinformatics databases and resources.

• fxtools

  • A barebones and fast fast[aq] manipulation CLI written in rust.

• pipspeak

  • A barebones and fast parser for PIPSeq data to make compatible with transcriptomics tools like Kallisto and Salmon.

• scispeak

  • A barebones and fast parser for sci-rna-seq3 data to make compatible with transcriptomics tools like Kallisto and Salmon.

• gtfjson

  • A GTF parsing CLI that outputs all annotation information inline with genome feature data as a newline-delim JSON. Also has some utilities for operating on the ndjson for various tasks.

• splici

  • A rust implementation of the splici algorithm to build spliced/unspliced reference transcriptomes used in RNA velocity.

Graph Theory and Network Motifs

• memoesu
  • A memoized and multithreaded implementation of the ESU algorithm for network motif discovery.
• graphtries
  • A rust implementation of the gtries subgraph enumeration algorithm for network motif discovery and searching.
• convg
  • A simple CLI for viewing and converting GRAPH6 and DIGRAPH6 formatted text between different formats.

Computational Drug Discovery

• ClusterDock
  • Pipeline and analysis scripts for k-mean based clustering of matching-spheres within DOCK for huge speed improvements.

Libraries

Sequencing + Genomics

• fxread
  • A fast and barebones fast[aq] parser focused on the iterator pattern.
• bedrs
  • A genomic interval arithmetic library for rust.
• gtftools
  • A fast parser for Ensembl-GTF formatted files.
• disambiseq
  • Creates unambiguous one-off mismatch libraries for DNA sequences. Useful for O(1) hashmap lookups with one-off mismatches.
• faiquery
  • Performs interval queries on an indexed fasta sequence. This is the backend used by gia get-fasta.

Statistics

• adjustp
  • A simple p-value adjustment library for rust.
• information
  • A library for performing information theoretic functions in rust.
• intc
  • A library for performing the *-INC algorithm for guide -> gene level p-value aggregation. Uses a Mann-Whitney U test of tests vs. control genes.
• alpha-rra
  • A library for performing the alpha-RRA algorithm for guide -> gene level p-value aggregation. Parameterizes a beta distribution against expected normalized ranks.

Graph Theory

• graph6-rs
  • A rust library for converting to and from graph6 formatted files from NAUTY
• graph-canon
  • Super fast and barebones graph canonicalization using nauty C-lib and built on petgraph.

Miscellaneous

• pvsvg
  • A python library to generate vis.js networks that can be exported as SVG

Pipelines

Single-Cell Sequencing

• pipseq_nextflow
  • Process PIPSeq reads using Kallisto.
• sciseq_rna_velocity_nextflow
  • Process sci-rna-seq3 reads using Kallisto and a splice-aware index
• 10x_nextflow
  • Processing 10X reads using Kallisto.
• 10x_rna_velocity_nextflow
  • Processing 10X reads using Kallisto and a splice-aware index

CRISPR Screening

• stagger sequencing crispr screens
  • A nextflow pipeline to map a CRISPR screen library using stagger sequencing technology

Resources

• howdoi

  • A collection of resources for bioinformatics analysese related to CRISPR screens. May expand to other things in the future.

• screen libraries

  • A collection of CRISPR screening libraries (H1-H7) used in the Kampmann lab. Compatible with sgcount.