Projects

mature

data-analysis langelab

SQuAPP

R 11 v0.30 public published

proteomics quantification visualization

R/Shiny app for quality control and quantitative analysis of proteins, peptides, and PTMs, built for researchers who do not code.

GitHub Docs App Paper

stable

data-analysis langelab

QuEStVar

Python 1 v0.1.0 public published

proteomics statistics equivalence-testing

Runs equivalence tests (TOST) beside differential tests to separate stable, changing, and undetermined proteins.

GitHub Analysis PyPI Docs Paper Blog

data-analysis langelab

pepVet

R 3 v0.99.1 public planned

proteomics peptides digestion

Proteolytic digest simulation, peptide-set scoring, and enzyme comparison for bottom-up proteomics.

GitHub Bioconductor Docs

data-analysis langelab

HarmonizePy

Python 1 v0.3.2 public na

batch-effect-correction missing-data multi-omics statistics

Pure-Python port of HarmonizR: batch-effect correction that tolerates missing values, checked against the R results.

GitHub Docs Blog

metadata langelab

pxseek

Python 2 v0.5.1 public na

proteomics metadata proteomexchange cli

Command-line tool to query, filter, and download ProteomeXchange dataset metadata, with a local cache.

GitHub PyPI Docs Blog

metadata langelab

PXAudit

Python 1 v0.6.0 public na

proteomics metadata open-data cli

Command-line tool that grades PRIDE datasets for reuse on six FAIR-readiness tiers and a quantification-readiness axis.

GitHub PyPI Docs

core-tooling personal

z-fasta

Zig 16 v0.4.0 public planned

bioinformatics fasta simd performance cli

FASTA indexing, region extraction, validation, and stats in a few MB of memory, writing samtools-compatible .fai indexes.

GitHub Docs Blog

core-tooling personal

zebrac

Zig 1 v0.6.3 public na

benchmarking performance linux cli

Linux command benchmarking on perf_event_open, with hardware counters, peak memory, and a terminal view. Extended from andrewrk/poop.

GitHub Blog

core-tooling personal

z-oci

Zig 1 v0.7.2 public na

oci container-registry library

Read-only client for the OCI and Docker registry API v2 in pure Zig, with digest checks and platform selection.

GitHub Docs

language-dev personal

z-toml

Zig 4 v0.4.1 public na

toml parser cli library

TOML 1.1.0 parser and rewrite toolkit for Zig: typed parsing, dynamic trees, and edits that keep untouched bytes.

GitHub Blog

active

data-analysis langelab

ProteoForge

Python 2 v0.0.4 public published

proteomics proteoforms statistics missing-data

Finds peptides that diverge from the rest of their protein across conditions and groups them into differential proteoforms, accounting for imputed values.

GitHub Analysis Paper Blog

data-analysis personal

loqculate

Python 6 v0.4.1 public planned

mass-spectrometry quantification calibration statistics

Estimates limits of detection and quantitation from mass spectrometry calibration curves, with bootstrap and delta-method intervals.

GitHub Docs

standards personal

mzArc

Zig 4 v0.3.0 public na

mass-spectrometry mzml compression codec

Compression for mzML that can keep the file byte-exact, in about 1 MiB of memory.

GitHub Blog

standards personal

mzValidate

Zig 4 v0.1.10 public na

mass-spectrometry mzml validator cli

One-pass, streaming mzML validator in Zig.

GitHub

standards personal

mzDiff

Zig v0.1.0 public na

mass-spectrometry mzml cli

Compares two mzML files by meaning, not bytes: pairs spectra in any order and rates each difference critical, major, or minor.

GitHub Docs

standards personal

zmz

Zig v0.1.0 public na

mass-spectrometry mzml parser performance library

mzML reader and writer for Zig that streams any file size in a few MiB of memory, with indexed lookup and MS-Numpress arrays.

GitHub Docs

core-tooling personal

z-fastq

Zig 2 v0.2.1 public na

bioinformatics fastq simd performance cli

Count, check, sample, interleave, and trim paired FASTQ in small, predictable memory, from one static binary.

GitHub Docs

core-tooling zenteomics

kanit

Zig 1 v0.7.0 public na

workflow-engines bioinformatics performance linux cli

Workflow engine for one Linux workstation: runs each step within its CPU and memory request, reruns only what changed, and keeps every attempt on record.

GitHub Docs

core-tooling personal

zipir

Zig v0.3.0 public na

compression file-formats library

gzip, zlib, DEFLATE, and BGZF for Zig in fixed, caller-owned memory, with no dependencies.

GitHub Docs

language-dev personal

z-xml

Zig 1 v0.2.0 public na

xml parser library

XML event reader, owned document model, and streaming UTF-8 writer for Zig, with bounded memory.

GitHub

wip

data-analysis personal

Maskomancy

Python v0.1.0 private na

unsupervised-learning pca missing-data proteomics

NIPALS PCA on matrices with missing values, without imputing them, checked against four reference implementations.

Source private

core-tooling personal

zamf

Zig v0.3.0 private na

bioinformatics bam performance cli

Reads, checks, filters, sorts, and repairs SAM and BAM files in about 1 MiB of working memory, from one static binary.

In development

early

standards personal

mzBridge

Zig private na

mass-spectrometry vendor-formats mzml conversion reverse-engineering

Reads Thermo .raw files and Bruker timsTOF .d directories without the vendor DLL or .NET, and writes indexed mzML.

Source private Blog

core-tooling personal

zpx

Zig private na

proteomics peptides digestion fasta

Digestion, decoys, and database checks that turn a protein FASTA into exactly defined peptide sets, in early development.

Not released yet

language-dev personal

zigR

Zig 2 v0.0.11 public na

r zig language-binding

Bridge for calling Zig code from R.

GitHub Blog

language-dev personal

zagplot

Zig v0.2.0 private na

plotting svg visualization

Plotting library and command-line tool in pure Zig that writes SVG.

Source private Blog

Tags by appearance: cli¹⁰ proteomics⁸ performance⁶ mass-spectrometry⁶ library⁵ mzml⁵ statistics⁴ bioinformatics⁴ missing-data³ parser³ quantification² visualization² peptides² digestion² metadata² fasta² simd² linux² compression² equivalence-testing¹ batch-effect-correction¹ multi-omics¹ proteomexchange¹ open-data¹ benchmarking¹ oci¹ container-registry¹ toml¹ proteoforms¹ calibration¹ codec¹ validator¹ fastq¹ workflow-engines¹ file-formats¹ xml¹ unsupervised-learning¹ pca¹ bam¹ vendor-formats¹ conversion¹ reverse-engineering¹ r¹ zig¹ language-binding¹ plotting¹ svg¹