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

VevestaX is an open source Python package for ML Engineers and Data Scientists.

VevestaX Track failed and successful experiments as well as features. VevestaX is an open source Python package for ML Engineers and Data Scientists.

24 Dec 14, 2022

A Pythonic introduction to methods for scaling your data science and machine learning work to larger datasets and larger models, using the tools and APIs you know and love from the PyData stack (such as numpy, pandas, and scikit-learn).

This tutorial's purpose is to introduce Pythonistas to methods for scaling their data science and machine learning work to larger datasets and larger models, using the tools and APIs they know and lo

102 Nov 10, 2022

ETL flow framework based on Yaml configs in Python

ETL framework based on Yaml configs in Python A light framework for creating data streams. Setting up streams through configuration in the Yaml file.

18 Jul 06, 2022

Autopsy Module to analyze Registry Hives based on bookmarks provided by EricZimmerman for his tool RegistryExplorer

13 Mar 31, 2022

Data Analytics: Modeling and Studying data relating to climate change and adoption of electric vehicles

Correlation-Study-Climate-Change-EV-Adoption Data Analytics: Modeling and Studying data relating to climate change and adoption of electric vehicles I

1 Jan 03, 2022

Orchest is a browser based IDE for Data Science.

Orchest is a browser based IDE for Data Science. It integrates your favorite Data Science tools out of the box, so you don’t have to. The application is easy to use and can run on your laptop as well

3.6k Jan 09, 2023

Creating a statistical model to predict 10 year treasury yields

Predicting 10-Year Treasury Yields Intitially, I wanted to see if the volatility in the stock market, represented by the VIX index (data source), had

10 Oct 27, 2021

ToeholdTools is a Python package and desktop app designed to facilitate analyzing and designing toehold switches, created as part of the 2021 iGEM competition.

ToeholdTools Category Status Repository Package Build Quality A library for the analysis of toehold switch riboregulators created by the iGEM team Cit

0 Dec 01, 2021

Repository created with LinkedIn profile analysis project done

EN/en Repository created with LinkedIn profile analysis project done. The datase

4 Aug 06, 2022

Display the behaviour of a realtime program with a scope or logic analyser.

1. A monitor for realtime MicroPython code This library provides a means of examining the behaviour of a running system. It was initially designed to

17 Dec 05, 2022

Conduits - A Declarative Pipelining Tool For Pandas

Conduits - A Declarative Pipelining Tool For Pandas Traditional tools for declaring pipelines in Python suck. They are mostly imperative, and can some

7 Nov 21, 2021

CubingB is a timer/analyzer for speedsolving Rubik's cubes, with smart cube support

CubingB is a timer/analyzer for speedsolving Rubik's cubes (and related puzzles). It focuses on supporting "smart cubes" (i.e. bluetooth cubes) for recording the exact moves of a solve in real time.

5 Sep 18, 2022

Option Pricing Calculator using the Binomial Pricing Method (No Libraries Required)

Binomial Option Pricing Calculator Option Pricing Calculator using the Binomial Pricing Method (No Libraries Required) Background A derivative is a fi

1 Nov 29, 2021

A set of procedures that can realize covid19 virus detection based on blood.

3 Mar 07, 2022

MEAD: A Large-scale Audio-visual Dataset for Emotional Talking-face Generation [ECCV2020]

MEAD: A Large-scale Audio-visual Dataset for Emotional Talking-face Generation [ECCV2020] by Kaisiyuan Wang, Qianyi Wu, Linsen Song, Zhuoqian Yang, Wa

112 Dec 28, 2022

A Python package for Bayesian forecasting with object-oriented design and probabilistic models under the hood.

Disclaimer This project is stable and being incubated for long-term support. It may contain new experimental code, for which APIs are subject to chang

1.6k Dec 29, 2022

A computer algebra system written in pure Python

SymPy See the AUTHORS file for the list of authors. And many more people helped on the SymPy mailing list, reported bugs, helped organize SymPy's part

9.9k Dec 31, 2022

TheMachineScraper 🐱‍👤 is an Information Grabber built for Machine Analysis

TheMachineScraper 🐱‍👤 is a tool made purely for analysing machine data for any reason.

5 Dec 01, 2022

A Python package for modular causal inference analysis and model evaluations

Causal Inference 360 A Python package for inferring causal effects from observational data. Description Causal inference analysis enables estimating t

506 Dec 19, 2022

Cold Brew: Distilling Graph Node Representations with Incomplete or Missing Neighborhoods

Cold Brew: Distilling Graph Node Representations with Incomplete or Missing Neighborhoods Introduction Graph Neural Networks (GNNs) have demonstrated

37 Dec 15, 2022