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HW1-FAST-AQ-Parser Public
Forked from BMI203-2025/HW1-FAST-AQ-ParserJupyter Notebook MIT License UpdatedJan 14, 2025 -
scez Public
Single Cell Analysis, Easy Mode!
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ezformer Public
Run enformer like models, get prediction tracks, and perform benchmarking
Python MIT License UpdatedJan 5, 2025 -
gget Public
Forked from pachterlab/gget🧬 gget enables efficient querying of genomic reference databases
Python BSD 2-Clause "Simplified" License UpdatedJan 4, 2025 -
BMI-206-Class-Project Public
SCENT (Tissue-specific enhancer-gene) | BMI-206 Class Project
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enformer_fine_tuning Public
Forked from shirondru/enformer_fine_tuningFor fine-tuning Enformer using paired WGS & gene expression data
Python UpdatedDec 6, 2024 -
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SuPreMo Public
Forked from ketringjoni/SuPreMoPipeline for generating reference and perturbed sequences for input into predictive models.
Jupyter Notebook UpdatedNov 18, 2024 -
awesome-CRISPR Public
Forked from davidliwei/awesome-CRISPRList of software/websites/databases/other stuff for genome engineering
MIT License UpdatedNov 8, 2024 -
RNAMultiOmics Public
A multi-omics analytic framework to study RNA dynamics
Python MIT License UpdatedOct 25, 2024 -
omicverse Public
Forked from Starlitnightly/omicverseA python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Jupyter Notebook GNU General Public License v3.0 UpdatedOct 17, 2024 -
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blitzgsea Public
Forked from MaayanLab/blitzgseaFast Gene Set Enrichment Analysis (GSEA) implementation of the prerank algorithm. Use Loess interpolation of bimodal ES distribution for accurate p-value estimation.
Jupyter Notebook Apache License 2.0 UpdatedSep 22, 2024 -
TDC Public
Forked from mims-harvard/TDCTherapeutics Data Commons: Artificial Intelligence Foundation for Therapeutic Science
Jupyter Notebook MIT License UpdatedJul 22, 2024 -
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PrimeKG Public
Forked from mims-harvard/PrimeKGPrecision Medicine Knowledge Graph (PrimeKG)
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cancer_data Public
Forked from kevinhu/cancer_dataA unified downloader+preprocessor for cancer genomics datasets
Python MIT License UpdatedJun 26, 2024 -
PyDESeq2 Public
Forked from owkin/PyDESeq2A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Python MIT License UpdatedJun 24, 2024 -
pypage Public
Forked from goodarzilab/pypagepython implementation of the PAGE algorithm
Python MIT License UpdatedJun 10, 2024 -
pvsvg Public
Forked from noamteyssier/pvsvga python wrapper of the vis.js network visualization library with an additional ability to export static SVG
JavaScript MIT License UpdatedMay 24, 2024 -
pager Public
PAGE algorithm run and downstream analysis
Jupyter Notebook MIT License UpdatedMar 30, 2024 -
PosSpacer Public archive
A framework for preprocessing multiplexed CRISPR libraries
Python MIT License UpdatedMar 9, 2024 -
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herken2022_originalcode Public
Forked from bherken/herken2024_originalcodeoriginal code for the manuscript "Environmental challenge rewires functional connections among human genes"
Jupyter Notebook UpdatedDec 30, 2023 -