BIMSB bioinformatics platform / Akalin Lab

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105 repositories

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
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MIT License
•28•0•0•0•Updated Nov 11, 2024Nov 11, 2024
VoltRon
Public
Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration
R
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Other
•10•41•1•0•Updated Nov 10, 2024Nov 10, 2024
ikarus
Public
Identifying tumor cells at the single-cell level using machine learning
machine-learning bioinformatics cancer-genomics single-cell
HTML
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MIT License
•12•44•2•0•Updated Nov 10, 2024Nov 10, 2024
ZarrDataFrame
Public
R
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MIT License
•1•0•0•0•Updated Nov 7, 2024Nov 7, 2024
ZarrArray
Public
Zarr backend for DelayedArray objects
R
•1•2•3•0•Updated Nov 7, 2024Nov 7, 2024
HDF5DataFrame
Public
R
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MIT License
•1•0•0•0•Updated Nov 3, 2024Nov 3, 2024
ImageArray
Public
R
•1•0•0•0•Updated Oct 30, 2024Oct 30, 2024
medLLMbenchmark
Public
Jupyter Notebook
•0•0•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
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Other
•3•14•0•0•Updated Oct 8, 2024Oct 8, 2024
flexynesis
Public
A deep-learning based multi-modal data integration suite that aims to achieve synesis in a flexible manner
Python
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Other
•4•21•10•0•Updated Oct 8, 2024Oct 8, 2024
pigx_rnaseq
Public
Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
snakemake pipeline rnaseq guix reproducibility
Python
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GNU General Public License v3.0
•12•21•22•0•Updated Oct 2, 2024Oct 2, 2024
mergenstudio
Public
R
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Other
•1•4•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
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GNU General Public License v3.0
•4•11•45•0•Updated Sep 12, 2024Sep 12, 2024
mergen
Public
AI-Driven Code Generation, Explanation and Execution for Data Analysis
R
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Other
•2•12•0•0•Updated Sep 11, 2024Sep 11, 2024
oncotrialLLM
Public
Python
•0•1•0•0•Updated Sep 3, 2024Sep 3, 2024
flexynesis_manuscript
Public
All publication material relevant for the manuscript describing the flexynesis software package
R
•0•1•0•0•Updated Aug 13, 2024Aug 13, 2024
pigx_docs
Public
Documentation for PiGx
documentation bioinformatics pipelines reproducibility pigx
JavaScript
•6•3•0•1•Updated Aug 7, 2024Aug 7, 2024
spatialNetSmooth
Public
R
•0•1•1•0•Updated Aug 5, 2024Aug 5, 2024
scregseg
Public
Single-cell regulatory landscape segmentation
Jupyter Notebook
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GNU General Public License v3.0
•2•5•1•1•Updated Aug 2, 2024Aug 2, 2024
spatialNetSmooth_scripts
Public
R
•0•1•0•0•Updated Jul 30, 2024Jul 30, 2024
flexynesis-benchmarks
Public
Comprehensive continuous benchmarking of tools for multi-omics data integration
Python
•1•1•2•0•Updated Jul 12, 2024Jul 12, 2024
scmaui-experiments
Public
Tutorials for scMaui
integration single-cell variational-autoencoder multiomics
Jupyter Notebook
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Other
•0•1•0•0•Updated Jun 17, 2024Jun 17, 2024
pigx-common
Public
Common infrastructure used by all PiGx pipelines
Python
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GNU General Public License v3.0
•1•0•2•1•Updated May 23, 2024May 23, 2024
netSmooth
Public
netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
bioinformatics genomics single-cell
HTML
•6•27•5•0•Updated May 15, 2024May 15, 2024
pigx_chipseq
Public
Pipeline for Analysis of ChIP-Seq data
snakemake pipeline guix reproducibility chipseq
Python
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GNU General Public License v3.0
•10•11•67•1•Updated May 8, 2024May 8, 2024
rcas-web
Public
Web interface for RCAS
JavaScript
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GNU Affero General Public License v3.0
•0•1•0•0•Updated May 8, 2024May 8, 2024
bimsbbioinfo.github.io
Public
website for the platform
HTML
•12•3•0•4•Updated May 3, 2024May 3, 2024
uyar_et_al_multiomics_deeplearning
Public
maui goes pancancer
R
•6•4•0•0•Updated Apr 19, 2024Apr 19, 2024
BayesPrism
Public
A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
HTML
•46•0•0•0•Updated Apr 15, 2024Apr 15, 2024
GEOparse
Public
Python library to access Gene Expression Omnibus Database (GEO)
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•52•0•0•0•Updated Apr 15, 2024Apr 15, 2024