Wei Shen (@shenwei356)
github

shenwei356

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  • Stars
    star
    4,415
  • Global Rank 6,318 (Top 0.3 %)
  • Followers 1,033
  • Following 304
  • Registered about 12 years ago
  • Most used languages
    Go
         65.1 %
    Python
         11.6 %
    Perl
         11.6 %
    R
         7.0 %
    HTML
         2.3 %
    Nextflow     2.3 %
  • Location ๐Ÿ‡จ๐Ÿ‡ณ China
  • Country Total Rank 1,225
  • Country Ranking
    Nextflow     5
    Perl
         16
    R
         70
    Go
         98
    Python
         6,615

Top repositories

1

seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Go
1,066
star
2

csvtk

A cross-platform, efficient and practical CSV/TSV toolkit in Golang
Go
882
star
3

awesome

Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.
568
star
4

taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies
Go
256
star
5

brename

A practical cross-platform command-line tool for safely batch renaming files/directories via regular expression
Go
224
star
6

kmcp

Accurate metagenomic profiling && Fast large-scale sequence/genome searching
Go
139
star
7

LexicMap

LexicMap: efficient sequence alignment against millions of prokaryotic genomes
Go
96
star
8

bio_scripts

Practical, reusable scripts for bioinformatics
Perl
90
star
9

bio

A lightweight and high-performance bioinformatics package in Golang
Go
83
star
10

unikmer

Toolkit for k-mer with taxonomic information
Go
53
star
11

ClipboardTextJoiner

Monitoring system clipboard change and joining multi-line text. It's very useful when copying multi-line text from PDF files.
Perl
47
star
12

go4bio

Golang for Bioinformatics
31
star
13

gtdb-taxdump

GTDB taxonomy taxdump files with trackable TaxIds
R
28
star
14

easy_qsub

Easily submitting multiple PBS jobs or running local jobs in parallel. Multiple input files supported.
Python
27
star
15

countminsketch

An implementation of Count-Min Sketch in Golang
Go
24
star
16

taxid-changelog

NCBI taxonomic identifier (taxid) changelog, including taxids deletion, new adding, merge, reuse, and rank/name changes.
R
19
star
17

bwt

Burrows-Wheeler Transform and FM-index in golang
Go
18
star
18

cnote

A platform independent command line note app
Go
17
star
19

gtaxon

gTaxon - a fast cross-platform NCBI taxonomy data querying (gi2taxid, taxid2taxon, name2taxid, LCA) tool, with cmd client and REST API server for both local and remote server.
Go
15
star
20

easy_sbatch

easy_sbatch - Batch submitting Slurm jobs with script templates
Python
14
star
21

ncbi_acc2gtdb_acc

Mapping NCBI Genbank accession to GTDB accession
14
star
22

strobemers

A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)
Go
14
star
23

ictv-taxdump

NCBI-style taxdump files for International Committee on Taxonomy of Viruses (ICTV)
12
star
24

crun

Run workflow mixed with concurrent and sequential jobs. Please use https://github.com/shenwei356/rush
Go
10
star
25

breader

breader (Buffered File Reader), asynchronous parsing and pre-processing while reading file. Safe cancellation is also supported.
Go
9
star
26

pinyin

ๆ”ถ้›†ๆฑ‰ๅญ—๏ผŒ็ป“ๅˆๆฑ‰่ฏญๆ‹ผ้Ÿณๆฅๅ–ๅ
Python
8
star
27

lexichash

LexicHash in Golang
Go
8
star
28

pand

Bitwise AND on two byte-slices using SIMD instructions
Go
7
star
29

unik

A k-mer serialization package for Golang
Go
7
star
30

kmers

bit-packed k-mers methods for Golang
Go
7
star
31

install-windows

Windows็ณป็ปŸๅฎ‰่ฃ…็ป้ชŒ
6
star
32

perfect-bioinformatic-tools

What should perfect bioinformatic tools be like?
6
star
33

breseq-rm-bg

Removing control/background mutations from breseq output index.html
Go
5
star
34

bbuffer

An alternative of standard library bytes.Buffer
Go
5
star
35

dirsize

Summarize size of directories and files in directories
Go
5
star
36

datakit

CSV/TSV file manipulation and more. Please use my another tool: csvtk, https://github.com/shenwei356/csvtk
Python
4
star
37

util

Golang utility packages
Go
4
star
38

uint64-hash-bench

Benchmark of three uint64 hash functions
Go
3
star
39

simhash-eval

Go
2
star
40

sun2021-cami-profiles

Ground truth metagenomic profiles in CAMI format for the 25 metagenomic reads in Sun et al.
2
star
41

go-hashing-kmer-bench

Benchmark of hashing k-mers in Golang
Go
2
star
42

shenwei356

2
star
43

RNA-HairpinFigure

Draw hairpin-like text figure from RNA sequence and its secondary structure in dot-bracket notation.
Perl
2
star
44

BioUtil

Bioinformatics Perl modules
Perl
2
star
45

rust-practice

Some tools in Rust for learning
2
star
46

todo

A very simple online todo list application
Go
1
star
47

blast-nf

A nextflow-based BLAST command-line helper tool
Nextflow
1
star
48

easy_run

Run command with default options in configuration file
Python
1
star
49

swr

Wei Shen' R utilities
R
1
star
50

shenwei356.github.io

HTML
1
star
51

uintset

Fast uint64 Set in golang
Go
1
star
52

process_queue

Process queue for high CPU/RAM/time usage processes
Perl
1
star
53

roux2016-mock-virome-cami-profile

Ground truth metagenomic profiles in CAMI format for the mock virome communities in Roux et al.
1
star