JetBrains-Research

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203 repositories

chipseq-smk-pipeline
Public
ChIP-Seq processing pipeline on snakemake
visualization quality-control snakemake pipeline chip-seq atac-seq peak-calling
Python
•2•5•4•0•Updated Jul 22, 2025Jul 22, 2025
kinference
Public
Running ONNX models in vanilla Kotlin
kotlin machine-learning neural-networks onnx
Kotlin
•
Apache License 2.0
•7•183•6•1•Updated Jul 22, 2025Jul 22, 2025
omnipeak
Public
A universal HMM-based peak caller capable of processing a broad range of ChIP-seq, ATAC-seq, and single-cell ATAC-seq datasets of different quality.
Kotlin
•
MIT License
•0•2•0•0•Updated Jul 22, 2025Jul 22, 2025
bioinf-commons
Public
Bioinformatics library in Kotlin
hmm bioinformatics progress methylation dataset fasta chip-seq sampling bed bam
Kotlin
•
MIT License
•3•33•1•0•Updated Jul 22, 2025Jul 22, 2025
kinference-primitives
Public
Kotlin
•
Apache License 2.0
•0•5•0•0•Updated Jul 22, 2025Jul 22, 2025
EnvBench
Public
[DL4C @ ICLR 2025] A Benchmark for Automated Environment Setup
Python
•
MIT License
•3•18•0•0•Updated Jul 22, 2025Jul 22, 2025
fishbone
Public
Fishbone Ishikawa diagrams construction and visualising
JavaScript
•
MIT License
•0•4•3•0•Updated Jul 22, 2025Jul 22, 2025
rocqstar-rag
Public
BigRocq is a utility, that takes a Rocq (former Coq) project as input and uses domain knowladge to increase a number of theorems in the dataset by a significant factor.
coq code-generation dataset-augmentation rocq coq-lsp
TypeScript
•0•4•0•4•Updated Jul 22, 2025Jul 22, 2025
Mutassertix
Public
Kotlin
•0•0•0•0•Updated Jul 21, 2025Jul 21, 2025
viktor
Public
Efficient f64-only ndarray in Kotlin
Kotlin
•
MIT License
•6•129•15•1•Updated Jul 21, 2025Jul 21, 2025
span-analysis
Public
Datasets analysis and comparison scripts for SPAN semi-supervised peak analyzer
Jupyter Notebook
•0•0•0•0•Updated Jul 18, 2025Jul 18, 2025
span
Public
SPAN Peak Analyzer
bioinformatics chip-seq peak-caller
Kotlin
•
MIT License
•1•9•2•0•Updated Jul 18, 2025Jul 18, 2025
edm-workshop-tasks
Public
Kotlin
•0•0•0•0•Updated Jul 16, 2025Jul 16, 2025
jbr
Public
JBR Genome Browser
genome-browser
Dockerfile
•1•11•105•0•Updated Jul 16, 2025Jul 16, 2025
kotlinx.fuzz
Public
Fuzzer for Kotlin libraries
Kotlin
•
Apache License 2.0
•4•95•5•0•Updated Jul 15, 2025Jul 15, 2025
verified-cogen
Public
Repo for PLAN's verified code generation project
Rust
•2•8•0•2•Updated Jul 8, 2025Jul 8, 2025
KOALA
Public
Kotlin
•
MIT License
•0•9•8•2•Updated Jun 26, 2025Jun 26, 2025
federated-compute-server-odp
Public
Java
•
Apache License 2.0
•4•1•0•0•Updated Jun 11, 2025Jun 11, 2025
ase2025-starter-kit
Public
Python
•
MIT License
•19•21•0•0•Updated Jun 10, 2025Jun 10, 2025
coqpilot
Public
VSCode extension that is designed to help automate writing of Coq proofs.
coq formal-methods code-generation theorem-prover llm
TypeScript
•
GNU Lesser General Public License v2.1
•4•109•1•0•Updated Jun 8, 2025Jun 8, 2025
pubtrends
Public
Scientific literature explorer. Runs a Pubmed or Semantic Scholar search and allows user to explore high-level structure of result papers
pubmed bibliometrics semantic-scholar
Python
•
Apache License 2.0
•4•45•44•1•Updated Jun 7, 2025Jun 7, 2025
YouTokenToMe
Public
Unsupervised text tokenizer focused on computational efficiency
C++
•
MIT License
•105•5•0•2•Updated Jun 5, 2025Jun 5, 2025
git-good-bench
Public
Repository accompanying our REALM '25 publication: "GitGoodBench: A Novel Benchmark For Evaluating Agentic Performance On Git"
Jupyter Notebook
•
Apache License 2.0
•0•2•1•0•Updated May 29, 2025May 29, 2025
rocqstar-agentic-system
Public
TypeScript
•
GNU Lesser General Public License v2.1
•0•4•0•0•Updated May 28, 2025May 28, 2025
TestSpark
Public
TestSpark - a plugin for generating unit tests. TestSpark natively integrates different AI-based test generation tools and techniques in the IDE. Started by SERG TU Delft. Currently under implementation by JetBrains Research (Software Testing Research) for research purposes.
Kotlin
•
MIT License
•26•75•33•6•Updated May 28, 2025May 28, 2025
EDAplot
Public
VegaChat paper: Generating and Evaluating Declarative Charts Using Large Language Models
Python
•0•0•0•0•Updated May 23, 2025May 23, 2025
project-adaptation-experiments
Public
Python
•0•2•0•0•Updated May 23, 2025May 23, 2025
learned-retrieval
Public
Python
•0•1•0•0•Updated May 23, 2025May 23, 2025
litmuskt
Public
Litmus testing tool for Kotlin/Native (WIP)
Kotlin
•1•10•2•1•Updated Apr 22, 2025Apr 22, 2025
snakecharm
Public
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
bioinformatics-pipeline bioinformatics-tool python snakemake intellij pycharm intellij-plugins
Python
•
MIT License
•8•62•122•2•Updated Apr 18, 2025Apr 18, 2025