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Massachusetts General Hospital/Broad Institute

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Chenhao Li's starred repositories

Umi-OCR

OCR software, free and offline. 开源、免费的离线OCR软件。支持截屏/批量导入图片，PDF文档识别，排除水印/页眉页脚，扫描/生成二维码。内置多国语言库。

Language:PythonMIT22866 133 486

emoji-cheat-sheet

A markdown version emoji cheat sheet

Language:TypeScriptMIT12077 127 120

Wudao-dict

有道词典的命令行版本，支持英汉互查和在线查询。

Language:Python1116 36 85

MIT6.828_OS

MIT 6.828 Operating System Lab https://pdos.csail.mit.edu/6.828/2018/schedule.html

Language:CGPL-3.0984 6 3

training-collection

Collection of bioinformatics training materials

Language:PythonNOASSERTION940 42 68

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

Language:CGPL-3.0695 20 268

Online_R_learning

Online R learning for applied statistics

CC0-1.0456 17 3

qs

Quick serialization of R objects

Language:C386 13 86

genomepy

genes and genomes at your fingertips

Language:PythonMIT366 6 120

zeallot

Variable assignment with zeal! (or multiple, unpacking, and destructuring assignment in R)

Language:RNOASSERTION252 9 51

kingfisher-download

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

Language:PythonGPL-3.0231 7 32

awesome-nanopore

A curated list of awesome nanopore analysis tools.

scCustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

Language:RGPL-3.0183 3 165

genomad

geNomad: Identification of mobile genetic elements

Language:PythonNOASSERTION169 5 106

nanoseq

Nanopore demultiplexing, QC and alignment pipeline

Language:NextflowMIT152 135 71

skani

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

Language:RustMIT150 5 26

run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

Language:PythonGPL-3.0130 5 151

sylph

ultrafast genome querying and taxonomic profiling for metagenomic samples by abundance-corrected minhash.

Language:RustMIT122 2 11

taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Language:NextflowMIT104 148 190

eyedroppeR

Pick colours from an image in R

Language:RNOASSERTION63 2 2

voyager

From geospatial to spatial -omics

Language:RArtistic-2.061 4 32

fanyi

Translate Words or Sentences via Online Translators

Language:R40 2 16

anndataR

AnnData interoperability in R

Language:RNOASSERTION39 7 64

ggsc

🧠 Visualizing Single Cell and Spatial Transcriptomics

Language:R32 4 1

ggtraces

A tidyverse and grammar of graphics powered line traces visualizer

MIT26 20

mini3di

A NumPy port of the foldseek code for encoding protein structures to 3di.

Language:PythonGPL-3.019 2 2

MDPI_explorer

A simple package to explore MDPI´s articles by journal. A series of functions help to obtain lists of papers, obtain data from them (turnaround times, special issues and articles types) and create summary graphs.

Language:RNOASSERTION18 2 1

spatial

Single-Cell Spatial Explorer

Language:GoGPL-3.014 30

xgt

Efficient and fast querying and parsing of GTDB's data

Language:RustApache-2.013 10

ggnested

ggplots for nested data

Language:R8 2 1