Awesome bioinfomatics tools

Jeason

457字约2分钟

2024-05-10

gtf

GffRead: GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

genomepy genomepy is designed to provide a simple and straightforward way to download and use genomic data. This includes (1) searching available data, (2) showing the available metadata, (3) automatically downloading, preprocessing and matching data and (4) generating optional aligner indexes. All with sensible, yet controllable defaults. Currently, genomepy supports Ensembl, UCSC, NCBI and GENCODE.
mosdepth 快速计算测序深度

eggNOG-mapper Fast genome-wide functional annotation through orthology assignment

singleCellTK R interface to several popular single-cell RNA-sequencing (scRNAseq) data preprocessing, quality control, analysis, and visualization tools.
SnapATAC2 A Python/Rust package for single-cell epigenomics analysis
scDIOR single-cell data transformation between platforms of R and Python based on Hierarchical Data Format Version 5
cNMF inferring gene expression programs from scRNA-Seq
SCEVAN R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
Scanorama batch-correction and integration of heterogeneous scRNA-seq datasets
cellqc standardized quality control pipeline of single-cell RNA-Seq data

scCATCH Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Compass In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes

Lazy Predict Lazy Predict help build a lot of basic models without much code and helps understand which models works better without any parameter tuning