Common bioinformatics database construction

Last update: Jan 04, 2022

Related tags

Data Analysis biodb

Overview

biodb

Common bioinformatics database construction

1.taxonomy （Substance classification database）

Download the database

wget -c https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz
tar -zxvf new_taxdump.tar.gz
lineage2tax.py fullnamelineage.dmp >species.taxonomy
get_taxid.py rankedlineage.dmp --kingdom Bacteria >Bacteria.taxid

2.Rfam

Download the database

family.txt gunzip Rfam.cm.gz cmpress Rfam.cm ">

wget -c https://ftp.ebi.ac.uk/pub/databases/Rfam/14.6/Rfam.cm.gz
wget -c https://ftp.ebi.ac.uk/pub/databases/Rfam/14.6/rfam2go/rfam2go
wget -c https://ftp.ebi.ac.uk/pub/databases/Rfam/14.6/database_files/family.txt.gz
zcat family.txt.gz |awk -F '\t' '{print $1"\t"$2"\t"$4"\t"$19"\t"$30}' >family.txt
gunzip Rfam.cm.gz
cmpress Rfam.cm

Owner

sy520

Xingguo Zhang

GitHub Repository

Maximum Covariance Analysis in Python

xMCA | Maximum Covariance Analysis in Python The aim of this package is to provide a flexible tool for the climate science community to perform Maximu

39 Jan 03, 2023

A Python 3 library making time series data mining tasks, utilizing matrix profile algorithms

MatrixProfile MatrixProfile is a Python 3 library, brought to you by the Matrix Profile Foundation, for mining time series data. The Matrix Profile is

302 Dec 29, 2022

Processo de ETL (extração, transformação, carregamento) realizado pela equipe no projeto final do curso da Soul Code Academy.

1 Feb 03, 2022

Numerical Analysis toolkit centred around PDEs, for demonstration and understanding purposes not production

Numerics Numerical Analysis toolkit centred around PDEs, for demonstration and understanding purposes not production Use procedure: Initialise a new i

1 Nov 13, 2021

Modular analysis tools for neurophysiology data

Neuroanalysis Modular and interactive tools for analysis of neurophysiology data, with emphasis on patch-clamp electrophysiology. Functions for runnin

5 Dec 22, 2021

Feature engineering and machine learning: together at last

Feature engineering and machine learning: together at last! Lambdo is a workflow engine which significantly simplifies data analysis by unifying featu

14 Sep 15, 2022

First steps with Python in Life Sciences

First steps with Python in Life Sciences This course material is part of the "First Steps with Python in Life Science" three-day course of SIB-trainin

22 Jan 08, 2023

CS50 pset9: Using flask API to create a web application to exchange stocks' shares.

C$50 Finance In this guide we want to implement a website via which users can “register”, “login” “buy” and “sell” stocks, like below: Background If y

1 Jan 24, 2022

Average time per match by division

HW_02 Unzip matches.rar to access .json files for matches. Get an API key to access their data at: https://developer.riotgames.com/ Average time per m

11 Jan 07, 2022

Building house price data pipelines with Apache Beam and Spark on GCP

This project contains the process from building a web crawler to extract the raw data of house price to create ETL pipelines using Google Could Platform services.

1 Nov 22, 2021

Instant search for and access to many datasets in Pyspark.

SparkDataset Provides instant access to many datasets right from Pyspark (in Spark DataFrame structure). Drop a star if you like the project. 😃 Motiv

31 Dec 16, 2022

Python Practicum - prepare for your Data Science interview or get a refresher.

Python-Practicum Python Practicum - prepare for your Data Science interview or get a refresher. Data Data visualization using data on births from the

1 Jul 27, 2021

Get mutations in cluster by querying from LAPIS API

Cluster Mutation Script Get mutations appearing within user-defined clusters. Usage Clusters are defined in the clusters dict in main.py: clusters = {

1 Oct 22, 2021

This module is used to create Convolutional AutoEncoders for Variational Data Assimilation

VarDACAE This module is used to create Convolutional AutoEncoders for Variational Data Assimilation. A user can define, create and train an AE for Dat

23 Dec 16, 2022

wikirepo is a Python package that provides a framework to easily source and leverage standardized Wikidata information

Python based Wikidata framework for easy dataframe extraction wikirepo is a Python package that provides a framework to easily source and leverage sta

35 Jan 04, 2023

Bearsql allows you to query pandas dataframe with sql syntax.

Bearsql adds sql syntax on pandas dataframe. It uses duckdb to speedup the pandas processing and as the sql engine

14 Jun 22, 2022

NumPy and Pandas interface to Big Data

Blaze translates a subset of modified NumPy and Pandas-like syntax to databases and other computing systems. Blaze allows Python users a familiar inte

3.1k Jan 05, 2023

The OHSDI OMOP Common Data Model allows for the systematic analysis of healthcare observational databases.

14 Jan 02, 2023

Finding project directories in Python (data science) projects, just like there R rprojroot and here packages

Find relative paths from a project root directory Finding project directories in Python (data science) projects, just like there R here and rprojroot

102 Nov 16, 2022

Kats, a kit to analyze time series data, a lightweight, easy-to-use, generalizable, and extendable framework to perform time series analysis, from understanding the key statistics and characteristics, detecting change points and anomalies, to forecasting future trends.

Description Kats is a toolkit to analyze time series data, a lightweight, easy-to-use, and generalizable framework to perform time series analysis. Ti

4.1k Jan 09, 2023