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a-deep-learning-model-for-predicting-next-generation-sequencing-depth-from-dna-sequence

A Deep Learning Model for Predicting Next-Generation Sequencing Depth from DNA Sequence

agape

AGAPE (Automated Genome Analysis PipelinE) for yeast pan-genome analysis

airrflow

B-cell and T-cell Adaptive Immune Receptor Repertoire (AIRR) sequencing analysis pipeline using the Immcantation framework

alphafold_non_docker

AlphaFold2 non-docker setup

analysing-10x-scrna-data-wang-et-al-2020-nat-commun-

I redo the ScRNA analysis in the paper of Wang et al 2020, Nat Comm. Here's my modified script for Helen He Zhu github (https://github.com/HelenHeZhu/StemCell)

asp_pan

Generating large pangenome for Aspergillus fumigatus

atac-seq-pipeline

ENCODE ATAC-seq pipeline

atacseq

ATAC-seq analysis pipeline

atacseq-1

ATAC-seq peak-calling, QC and differential analysis pipeline.

audio-data-analysis-using-deep-learning

Audio data analysis using Deep Learning.

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

awesome-deep-learning-papers

The most cited deep learning papers

awesome-knowledge-distillation

Awesome Knowledge-Distillation. 分类整理的知识蒸馏paper(2014-2021)。

awesome-machine-learning-cn

机器学习资源大全中文版，包括机器学习领域的框架、库以及软件

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

bayesian-machine-learning

Notebooks about Bayesian methods for machine learning

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bioinfokit

Bioinformatics data analysis and visualization toolkit

bioseq2vec

BioSeq2vec: learning deep representation of biological sequences using LSTM Encoder-Decoder

broad-fungalgroup

Broad Fungal Genomics group scripts

c-plus-plus

Collection of various algorithms in mathematics, machine learning, computer science and physics implemented in C++ for educational purposes.

cgat

Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps

chatglm-finetuning

基于ChatGLM-6B模型，进行下游具体任务微调，涉及Freeze、Lora、P-tuning等

chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

chip-seq-pipeline2

chip-seq_tutorial

ChIP-Seq Analysis Tutorial

chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline

chloroplast-genome-assembly

A pipeline for assemble chroloplast genome using short/long reads

clam

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

cmonkey2

Python port of cMonkey, a machine-learning based method for clustering