flyboyleo

alphafold

Open source code for AlphaFold.

catboost

A fast, scalable, high performance Gradient Boosting on Decision Trees library, used for ranking, classification, regression and other machine learning tasks for Python, R, Java, C++. Supports computation on CPU and GPU.

Google-Assistant-Unofficial-Desktop-Client

A cross-platform unofficial Google Assistant Client for Desktop (powered by Google Assistant SDK)

NCRFpp

NCRF++, a Neural Sequence Labeling Toolkit. Easy use to any sequence labeling tasks (e.g. NER, POS, Segmentation). It includes character LSTM/CNN, word LSTM/CNN and softmax/CRF components.

alphafold2

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

cdhit

Automatically exported from code.google.com/p/cdhit

rmsd

Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

renrenBackup

A backup tool for renren.com

alphafold_non_docker

AlphaFold2 non-docker setup

TRUST4

TCR and BCR assembly from RNA-seq data

DeepDock

Code related to : O. Mendez-Lucio, M. Ahmad, E.A. del Rio-Chanona, J.K. Wegner, A Geometric Deep Learning Approach to Predict Binding Conformations of Bioactive Molecules

scCODA

A Bayesian model for compositional single-cell data analysis

Uni-Fold

DLEPS

A Deep Learning based Efficacy Prediction System for drug discovery

NanoNet

Codon_Optimization

https://www.nature.com/articles/s41598-020-74091-z#Tab1

annotate_v

Antibody Annotation - Annotate VH and VL sequences (FR and CDR) in Python

sc3s

Single Cell Consensus Clustering with Speed

DestVI-reproducibility

Reproducing the experiments of the DestVI paper

smartseq2

A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.

CellR

CellR: single-cell RNA-Seq guided deconvolution of cellular composition from bulk-tissue RNA-Seq

ASAP-SML

ASAP-SML: An Antibody Sequence Analysis Pipeline Using Statistical Testing and Machine Learning

STARsoloManuscript

Code for analyses in the STARsolo manuscript

two-stage-cox-nnet

solo-in-drops

STARsolo wrapper for inDrops analysis

BASE

Brain Antibody Sequence Evaluation

STARSolo10X

STARSolo test on 10X data

nanoprofiler

Profiling Nanobodies sequencing libraries

nanobody_fitness

code to analyze single-domain antibody (nanobody) stability from sequencing and cytometry data

pcrm2