Sancar Adali's repositories
deeplearning-models
A collection of various deep learning architectures, models, and tips
deeplexicon
Signal based nanopore RNA demultiplexing with convolutional neural networks
pySAR_proteinseq_aa
Analysing Sequence Activity Relationships (SARs) of protein sequences and their mutants using Machine Learning.
ReLSO-Guided-Generative-Protein-Design-using-Regularized-Transformers
a Transformer-based neural network for generating highly optimized protein sequences called Regularized Latent Space Optimization (RELSO)
awesome-awesomeness
A curated list of awesome awesomeness
aaindex
Python package for AAIndex database (https://www.genome.jp/aaindex/)
ASHURE
Python-based pipeline for analyzing Nanopore sequencing metabarcoding data
bio-transformers
bio-transformers is a wrapper on top of the ESM/Protbert model, trained on millions on proteins and used to predict embeddings.
biotools
A list of useful bioinformatics resources
configurations-linux
My Linux Machine Configurations
deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
dgl-lifesci
Python package for graph neural networks in chemistry and biology
dms_tools2
software for the analysis and visualization of deep mutational scanning data
Enrich2
Tool for deep mutational scanning experiments.
EpiNano
Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)
EVE_fork
Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Joint collaboration between the Marks lab and the OATML group.
Genomic-ULMFiT
ULMFiT for Genomic Sequence Data
IsoSeq
IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
mutect2
Workflow to run Mutect2 (GATK4)
pbsv
pbsv - PacBio structural variant (SV) calling and analysis tools
rRNA_nanoSHAPE
Code accompanying "Direct detection of RNA modifications and structure using single molecule nanopore sequencing"
scientific-python-cookiecutter
a tutorial and 'cookiecutter' template for a scientific Python library
SEMAi
Spatial Epitope Modeling with Artificial intelligence (SEMA)
smrtsv2
Structural variant caller for PacBio
strelka
Strelka2 germline and somatic small variant caller
tombo
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.