BIMSB bioinformatics platform / Akalin Lab

All

111 repositories

VoltRon
Public
Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration
R
•
MIT License
•19•103•3•0•Updated Aug 4, 2025Aug 4, 2025
flexynesis
Public
A deep-learning based multi-modal data integration suite that aims to achieve synesis in a flexible manner
Python
•
Other
•14•57•12•0•Updated Aug 1, 2025Aug 1, 2025
compgen_course_2025_module3
Public
Compgen Course 2025, Module 3 Course Material, Multi-omics integration using deep learning
Jupyter Notebook
•26•62•0•0•Updated Aug 1, 2025Aug 1, 2025
deconvR
Public
The deconvR is an R package designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model.
regression omics dna-methylation deconvolution bioconductor-package
R
•3•10•0•0•Updated Jul 28, 2025Jul 28, 2025
flexynesis_manuscript
Public
Manuscript material for Flexynesis
R
•
MIT License
•0•2•0•0•Updated Jul 26, 2025Jul 26, 2025
flexynesis-benchmarks
Public
Comprehensive continuous benchmarking of tools for multi-omics data integration
Python
•1•2•2•0•Updated Jul 26, 2025Jul 26, 2025
ImageArray
Public
R
•
Other
•1•2•0•0•Updated Jul 5, 2025Jul 5, 2025
PocketVina
Public
GPU-accelerated protein-ligand docking with automated pocket detection, exploring through multi-pocket conditioning. Official Implementation of PocketVina
protein-ligand-docking drug-discovery molecular-biology protein-ligand-interactions protein-ligand-binding-affinity molecular-docking autodock-vina autodock-gpu p2rank quickvina
C++
•
MIT License
•7•61•2•1•Updated Jul 4, 2025Jul 4, 2025
collab_barleben_kolesnichenko_colitis
Public
Collaboration project with Luisa Barleben Kolesnichenko Lab - Acute Colitis in Mice
HTML
•0•0•0•0•Updated Jun 19, 2025Jun 19, 2025
scregseg
Public
Single-cell regulatory landscape segmentation
Jupyter Notebook
•
GNU General Public License v3.0
•2•5•1•0•Updated Jun 3, 2025Jun 3, 2025
guix-bimsb
Public
Packages for GNU Guix that have not yet or will not be submitted upstream for various reasons
bioinformatics hpc guix package-management scheme gnu-guix
Scheme
•
GNU General Public License v3.0
•4•16•0•0•Updated May 23, 2025May 23, 2025
anglemania
Public
Improved feature extraction for scRNA-seq dataset integration.
R
•
GNU General Public License v3.0
•0•1•5•0•Updated May 14, 2025May 14, 2025
HDF5DataFrame
Public
R
•
Other
•1•0•0•0•Updated May 3, 2025May 3, 2025
rstudio
Public
RStudio is an integrated development environment (IDE) for R
Java
•
Other
•1.1k•0•0•0•Updated Apr 18, 2025Apr 18, 2025
OncoLLMBenchmark
Public
Python
•0•1•0•0•Updated Apr 15, 2025Apr 15, 2025
genomation
Public
R package for genomic feature analysis and visualization
HTML
•24•79•37•1•Updated Apr 15, 2025Apr 15, 2025
ZarrDataFrame
Public
R
•
MIT License
•1•0•0•0•Updated Apr 14, 2025Apr 14, 2025
pigx-common
Public
Common infrastructure used by all PiGx pipelines
Python
•
GNU General Public License v3.0
•1•0•2•2•Updated Apr 3, 2025Apr 3, 2025
guix-bimsb-nonfree
Public
GNU Guix package definitions for proprietary software, or software with unclear licenses.
scheme bioinformatics hpc guix package-management gnu-guix
Scheme
•
GNU General Public License v3.0
•3•12•0•0•Updated Feb 20, 2025Feb 20, 2025
oncotrialLLM
Public
Python
•3•3•0•0•Updated Feb 15, 2025Feb 15, 2025
compgen
Public
1•0•0•0•Updated Dec 28, 2024Dec 28, 2024
pigx_rnaseq
Public
Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
snakemake pipeline rnaseq guix reproducibility
Python
•
GNU General Public License v3.0
•12•20•23•0•Updated Dec 27, 2024Dec 27, 2024
ZarrArray
Public
Zarr backend for DelayedArray objects
R
•1•2•3•0•Updated Dec 15, 2024Dec 15, 2024
tibanna-bimsb
Public
Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
Python
•
MIT License
•28•0•0•0•Updated Dec 5, 2024Dec 5, 2024
pigx_scrnaseq
Public
Pipeline for analysis of Dropseq single cell data
guix snakemake-workflows dropseq single-cell-rna-seq
Python
•6•11•29•0•Updated Nov 14, 2024Nov 14, 2024
ikarus
Public
Identifying tumor cells at the single-cell level using machine learning
machine-learning bioinformatics cancer-genomics single-cell
HTML
•
MIT License
•12•48•1•0•Updated Nov 10, 2024Nov 10, 2024
medLLMbenchmark
Public
Jupyter Notebook
•4•4•0•0•Updated Oct 21, 2024Oct 21, 2024
CompassDock
Public
Official Implementation of CompassDock
drug-discovery molecular-biology protein-ligand-interactions molecular-docking drug-target-interactions binding-affinity
Python
•
Other
•3•20•0•0•Updated Oct 8, 2024Oct 8, 2024
mergenstudio
Public
R
•
Other
•1•5•0•0•Updated Sep 13, 2024Sep 13, 2024
pigx_bsseq
Public
bisulfite sequencing pipeline from fastq to methylation reports
bioinformatics guix reproducibility snakemake pipeline
Python
•
GNU General Public License v3.0
•4•12•46•0•Updated Sep 12, 2024Sep 12, 2024