Pinned Repositories
albert-bioinformatics-scripts
bbcfutils
Collection of stand-alone tools
bedSeq
A program to efficiently append sequences to bed files
cloudbiolinux
CloudBioLinux: configure virtual (or real) machines with tools for biological analyses
gMiner
Manuiplations and statistics on genomic data
GRO-seq
GROSeq, RNASeq, Exome Sequencing.
PIntron
A novel pipeline for gene-structure prediction based on spliced alignment of transcript sequences (ESTs and mRNAs) against a genomic sequence
pytools
some general useful python tools for genomics
RNA-seq-Graph
RNA-seq Graph Builder is a method to reconstruct the Isoform Graph of a gene from RNA-seq data, without the genome information, where such a graph is a representation of the variants of alternative splicing of the gene structure.
RNASeqMappingScripts3
hjanime's Repositories
hjanime/annotated_deep_learning_paper_implementations
🧑🏫 60 Implementations/tutorials of deep learning papers with side-by-side notes 📝; including transformers (original, xl, switch, feedback, vit, ...), optimizers (adam, adabelief, sophia, ...), gans(cyclegan, stylegan2, ...), 🎮 reinforcement learning (ppo, dqn), capsnet, distillation, ... 🧠
hjanime/awesome-deep-learning-4-life-sciences
A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).
hjanime/BMBL-analysis-notebooks
A collection of bioinformatics data analysis notebooks focused on providing examples of current best practices in single-cell analysis.
hjanime/cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
hjanime/d2l-zh
《动手学深度学习》：面向中文读者、能运行、可讨论。中英文版被70多个国家的500多所大学用于教学。
hjanime/deepmind-research
This repository contains implementations and illustrative code to accompany DeepMind publications
hjanime/dify
Dify is an open-source LLM app development platform. It has the core tech required to build AI-native apps, including RAG, agent capabilities, model management, observability and more, packaged into one intuitive interface.
hjanime/DNABERT_S
DNABERT_S: Learning Species-Aware DNA Embedding with Genome Foundation Models
hjanime/EasyPubMed
EasyPubMed is an extension to make new PubMed easy to use
hjanime/esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
hjanime/flash-attention
Fast and memory-efficient exact attention
hjanime/maui
Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit
hjanime/MOVE
MOVE (Multi-Omics Variational autoEncoder) for integrating multi-omics data and identifying cross modal associations
hjanime/oomycete-effector-prediction
hjanime/ORFik
hjanime/OrthoFinder
Phylogenetic orthology inference for comparative genomics
hjanime/OrthoSLC
OrthoSLC: A pipeline to get Orthologous Genes using Reciprocal Best Blast Hit (RBBH) Single Linkage Clustering, indenpendent of relational database management system
hjanime/protein_bert
hjanime/ProtTrans
ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
hjanime/Qwen-Audio
The official repo of Qwen-Audio (通义千问-Audio) chat & pretrained large audio language model proposed by Alibaba Cloud.
hjanime/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)
hjanime/Scientific-LLM-Survey
Scientific Large Language Models: A Survey on Biological & Chemical Domains
hjanime/taxonkit
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
hjanime/Ternary
Create ternary plots in R
hjanime/timm
PyTorch image models, scripts, pretrained weights -- ResNet, ResNeXT, EfficientNet, EfficientNetV2, NFNet, Vision Transformer, MixNet, MobileNet-V3/V2, RegNet, DPN, CSPNet, and more
hjanime/TVBox_live
TVbox直播接口，互联网直播源检索，验证提取高速直播源
hjanime/Tvlist-awesome-m3u-m3u8
直播源相关资源汇总 📺 💯 IPTV、M3U —— 勤洗手、戴口罩，祝愿所有人百毒不侵
hjanime/Uni-Fold
An open-source platform for developing protein models beyond AlphaFold.
hjanime/Uni-Mol
Official Repository for the Uni-Mol Series Methods
hjanime/vital