darsa's repositories
BMDSI_class_2024
Biomedical Data Science Initiative class - 2024
Accessing_public_genomic_data
Tutorials on accessing public reference and genomic data
APALYZER-test
APALYZER-test
Bioinformatics-paper-2020.12
Bioinformatics course related papers: sample code of deep learning application in Bioinformatics
Bioinformatics-with-Python-Cookbook-Second-Edition
Bioinformatics with Python Cookbook Second Edition, published by Packt
bioutils
Standalone utility scripts for bioinformatics
ChIPseqPipe
Components of an automated ChIPseq and ATACseq pipeline
Deep-Learning-DNA-Sequences
Deep learning for identifying important motifs in DNA sequences. Exploration of the structure of the human genome by training neural network architectures (CNN, LSTM, Attention).
Deep-Learning-for-Predicting-Transcription-Factor-Binding-Site-in-DNA-ML-in-Bioin-Summer-School-2020
This was a hands-on tutorial during a ML in Bioinformatics Summer School in 2020
deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
dragonn
A toolkit to learn how to model and interpret regulatory sequence data using deep learning.
flair
Full-Length Alternative Isoform analysis of RNA
Interactive-Enrichment-Analysis
A set of Shiny apps to provide interactive enrichment analysis and exploration of results.
MediProbe-Drug-Discovery
In the fields of drug discovery and development, machine learning techniques have been used for the development of novel drug candidates. The methods for designing drug targets and novel drug discovery now routinely combine machine learning and deep learning algorithms to enhance the efficiency, efficacy, and quality of developed outputs.
pipeline-transcriptome-de
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
PythonDataScienceHandbook
Python Data Science Handbook: full text in Jupyter Notebooks
rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
samql
SQL-like query language for the SAM/BAM file format
samutils
Standalone utility scripts for manipulating SAM files
SMILES_featurization
In this project at the Rostlab (TUM), I search for the best way to encode small molecules for deep learning applications. The basis are SMILES, therefore this is featurization of SMILES.
SQANTI3
Tool for the Quality Control of Long-Read Defined Transcriptomes
supervenn
supervenn: precise and easy-to-read multiple sets visualization in Python
tabletools
Miscellaneous scripts for manipulating table files
tensorflow-deep-learning
All course materials for the Zero to Mastery Deep Learning with TensorFlow course.