BamQuery provides RNA-seq quantification for a given peptide (from 8 to 11 residues) in chosen RNA-seq samples (single or bulk).

A Systematic and Dynamic Pipeline for Single-Cell RNA Sequencing Analysis

This work was published on Analytical Chemistry: Full-Spectrum Prediction of Peptides Tandem Mass Spectra using Deep Neural Network

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.

Report processing and protein quantification for MS-based proteomics

Overview of GDC Harmonization Workflows

Obtain submitted reads and clinical info associated with CPTAC3 cases

Community-curated tutorials and datasets for ML in proteomics

VirusScan Pipeline

科研工作专用ChatGPT拓展，特别优化学术Paper润色体验，支持自定义快捷按钮，支持markdown表格显示，Tex公式双显示，代码显示功能完善，新增本地Python工程剖析功能/自我剖析功能

Ultra-efficient and sensitive method to search for Open Reading Frames in spliced genomes guided by reference annotation to maximize protein similarity within genes.

Snakemake workflow for somatic mutation detection without matched normal samples

The official code repository for examples in the O'Reilly book 'Generative Deep Learning'

Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

📡 Simple and ready-to-use tutorials for TensorFlow

An Open Source Machine Learning Framework for Everyone

Tensors and Dynamic neural networks in Python with strong GPU acceleration

🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.

The codebase of the OpenMS project

Deep Learning for humans

Caffe: a fast open framework for deep learning.

A list of tools on proteomics using deep learning

TensorFlow Tutorial and Examples for Beginners (support TF v1 & v2)

《动手学深度学习》：面向中文读者、能运行、可讨论。中英文版被60个国家的400所大学用于教学。

MASIC generates selected ion chromatograms (SICs) for all of the parent ions chosen for fragmentation in an LC-MS/MS analysis, characterizing the peak(s) in each SIC, computing peak statistics incl…