zardda

panel

Panel: The powerful data exploration & web app framework for Python

Diffusion-Models-Papers-Survey-Taxonomy

Diffusion model papers, survey, and taxonomy

auto-subtitle

Automatically generate and overlay subtitles for any video.

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.

papers_for_protein_design_using_DL

List of papers about Proteins Design using Deep Learning

moses

Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models

video-subtitle-generator

视频音频生成字幕，生成srt文件。无需申请第三方API，本地实现音频转文本。基于Transformer的视频字幕生成框架。A GUI tool for generating subtitle from videos and generating srt files.

chroma

A generative model for programmable protein design

Complex-Network

复杂网络研究资源整理和基础知识学习

RoseTTAFold-All-Atom

delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

RoseTTAFold2NA

RoseTTAFold2 protein/nucleic acid complex prediction

bedops

:microscope: BEDOPS: high-performance genomic feature operations

vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

rf_diffusion_all_atom

Public RFDiffusionAA repo

rmats-turbo

PiFold

The official implementation of the ICLR'23 paper PiFold: Toward effective and efficient protein inverse folding.

protein-frame-flow

Fast protein backbone generation with SE(3) flow matching.

regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.

heme_binder_diffusion

QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis

PocketGen

Implementation of PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets

Frame2seq

Structure-conditioned masked language modeling for protein sequence design

MMDiff

Joint Sequence-Structure Generation of Nucleic Acid and Protein Complexes with SE(3)-Discrete Diffusion

MetaCerberus

Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data

paper_implementations

This repository holds my paper implementations made for my studies and my content production

RepeatOBserverV1

An R package to visualize chromosome scale repeat patterns and predict centromere locations.

SPLICE-q

SPLICE-q -- A Python tool for genome-wide SPLIcing Efficiency quantification from RNA-seq data.

Tutorial-BSA-Python

Tutorial for bulk segregant analysis using Python

BioPipelines

Pipelines used in bioinfomatic data processing or analysis