This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot.

Related tags

Data AnalysissuperSFS
Overview

superSFS

This is a tool for speculation of ancestral allel, calculation of sfs and drawing its bar plot. It is easy-to-use and runing fast. What you should prepare is the phased vcf file containg the data of populations you intrested and the outgroup, the outgroup name file, and the annotation file. Enjoy it!!!

It has four models:

0:Using all function, from original vcf data to sfs barplot
1: Only speculate the ancestral allel and output new vcf file using speculated allel as reference
2: Only count the frequency of derived allel in each snp of each population
3: Only draw bar polt of sfs using data generated from the results of calutation of sfs

Example:

Model 0: python superSFS 0 ogdir threshold vcfdir annodir modir coutdir plotdir group
Model 1: python superSFS 1 ogdir threshold vcfdir outdir
Model 2: python superSFS 2 annodir modir coutdir
Model 3: python superSFS 3 coutdir plotdir group

Explation for each parameter:

ogdir: direction of outgroup names file
threshold: a number that if the sum of variant allel in outpgroup greater than it,the variant allel will be counted as ancestral allel
vcfdir: direction of vcf data
vannodir: direction of annotation file with sample names in first column and group name in second colum. This file should has header in first row
vmodir: assign the output direction of generated vcf file using speculated allel as reference
countdir: assign the output direction of calculation of derived allels for each snp in each group
plotdir: assign the output direction of bar plot of sfs
group: the group that you want to analysis
A notebook to analyze Amazon Recommendation Review Dataset.

Amazon Recommendation Review Dataset Analyzer A notebook to analyze Amazon Recommendation Review Dataset. Features Calculates distinct user count, dis

isleki 3 Aug 22, 2022
PipeChain is a utility library for creating functional pipelines.

PipeChain Motivation PipeChain is a utility library for creating functional pipelines. Let's start with a motivating example. We have a list of Austra

Michael Milton 2 Aug 07, 2022
pyhsmm MITpyhsmm - Bayesian inference in HSMMs and HMMs. MIT

Bayesian inference in HSMMs and HMMs This is a Python library for approximate unsupervised inference in Bayesian Hidden Markov Models (HMMs) and expli

Matthew Johnson 527 Dec 04, 2022
Retentioneering 581 Jan 07, 2023
Py-price-monitoring - A Python price monitor

A Python price monitor This project was focused on Brazil, so the monitoring is

Samuel 1 Jan 04, 2022
Top 50 best selling books on amazon

It's a dashboard that shows the detailed information about each book in the top 50 best selling books on amazon over the last ten years

Nahla Tarek 1 Nov 18, 2021
CleanX is an open source python library for exploring, cleaning and augmenting large datasets of X-rays, or certain other types of radiological images.

cleanX CleanX is an open source python library for exploring, cleaning and augmenting large datasets of X-rays, or certain other types of radiological

Candace Makeda Moore, MD 20 Jan 05, 2023
Processo de ETL (extração, transformação, carregamento) realizado pela equipe no projeto final do curso da Soul Code Academy.

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

Débora Mendes de Azevedo 1 Feb 03, 2022
WAL enables programmable waveform analysis.

This repro introcudes the Waveform Analysis Language (WAL). The initial paper on WAL will appear at ASPDAC'22 and can be downloaded here: https://www.

Institute for Complex Systems (ICS), Johannes Kepler University Linz 40 Dec 13, 2022
PostQF is a user-friendly Postfix queue data filter which operates on data produced by postqueue -j.

PostQF Copyright © 2022 Ralph Seichter PostQF is a user-friendly Postfix queue data filter which operates on data produced by postqueue -j. See the ma

Ralph Seichter 11 Nov 24, 2022
t-SNE and hierarchical clustering are popular methods of exploratory data analysis, particularly in biology.

tree-SNE t-SNE and hierarchical clustering are popular methods of exploratory data analysis, particularly in biology. Building on recent advances in s

Isaac Robinson 61 Nov 21, 2022
A model checker for verifying properties in epistemic models

Epistemic Model Checker This is a model checker for verifying properties in epistemic models. The goal of the model checker is to check for Pluralisti

Thomas Träff 2 Dec 22, 2021
A program that uses an API and a AI model to get info of sotcks

Stock-Market-AI-Analysis I dont mind anyone using this code but please give me credit A program that uses an API and a AI model to get info of stocks

1 Dec 17, 2021
Additional tools for particle accelerator data analysis and machine information

PyLHC Tools This package is a collection of useful scripts and tools for the Optics Measurements and Corrections group (OMC) at CERN. Documentation Au

PyLHC 3 Apr 13, 2022
nrgpy is the Python package for processing NRG Data Files

nrgpy nrgpy is the Python package for processing NRG Data Files Website and source: https://github.com/nrgpy/nrgpy Documentation: https://nrgpy.github

NRG Tech Services 23 Dec 08, 2022
PCAfold is an open-source Python library for generating, analyzing and improving low-dimensional manifolds obtained via Principal Component Analysis (PCA).

PCAfold is an open-source Python library for generating, analyzing and improving low-dimensional manifolds obtained via Principal Component Analysis (PCA).

Burn Research 4 Oct 13, 2022
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 = {

neherlab 1 Oct 22, 2021
BErt-like Neurophysiological Data Representation

BENDR BErt-like Neurophysiological Data Representation This repository contains the source code for reproducing, or extending the BERT-like self-super

114 Dec 23, 2022
Hidden Markov Models in Python, with scikit-learn like API

hmmlearn hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models. For supervised learning learning of HMMs and

2.7k Jan 03, 2023
An orchestration platform for the development, production, and observation of data assets.

Dagster An orchestration platform for the development, production, and observation of data assets. Dagster lets you define jobs in terms of the data f

Dagster 6.2k Jan 08, 2023