songweizhi

songweizhi's Stars

• hehonghui/the-economist-ebooks

  经济学人(含音频)、纽约客、自然、新科学人、卫报、科学美国人、连线、大西洋月刊、国家地理等英语杂志免费下载,支持epub、mobi、pdf格式, 每周更新.

  Language:CSS9.9k

• scrapy/quotesbot

  This is a sample Scrapy project for educational purposes

  Language:Python1.3k713778

• kblin/ncbi-genome-download

  Scripts to download genomes from the NCBI FTP servers

  Language:Python96935145173

• deeptools/deepTools

  Tools to process and analyze deep sequencing data.

  Language:Python69143947212

• lh3/gfatools

  Tools for manipulating sequence graphs in the GFA and rGFA formats

  Language:C216173321

• linnabrown/run_dbcan

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

  Language:Python148715840

• EngqvistLab/Tome

  A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

  Language:Python543615

• ssolo/ALE

  Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.

  Language:C++4673615

• DavidBSauer/OGT_prediction

  Scripts for calculating features and regression of prokaryote OGT

  Language:Python252124

• fanglab/mbin

  mBin: a methylation-based binning framework for metagenomic SMRT sequencing reads

  Language:Python253153

• Linwei-Wu/Global-bacterial-diversity-in-WWTPs

  Language:R220018

• sishuowang/Solutions_Manual_CME2006_MESA2014

  A solutions manual for all excercises in the Ziheng Yang's two seminall books on statistical molecular evolution: Computational Molecular Evolution (Yang 2006) and Molecular Evolution: A Statistical Approach (Yang 2014).

  Language:Terra14103

• Tancata/phylo

  Helper scripts for making phylogenies

  Language:Python14235

• donovan-h-parks/biolib

  Python package for common tasks in bioinformatic.

  Language:Python13237

• jfass/apc

  (a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join

  Language:Perl11224

• Kzra/Simple-Circularise

  For a sequence or list of sequences, simple-circularise will circularise a linear sequence that should be circular but has been overlapped during assembly.

  Language:Python10211

• angelolimeta/BioSampleParser

  R tool for parsing .xml metadata obtained through NCBI BioSample into tabular format

  Language:R9011

• lauringlab/variant_pipeline

  Work on the variant_pipeline and initial r analysis used in calling variants from NGS data

  Language:Python85813

• AADavin/ALEtutorial

  A tutorial on Phylogenetic Reconciliations using ALE

  Language:Jupyter Notebook7520

• amnona/SpongeEMP

  the sponge microbiome database

  Language:Python6401

• bzamecnik/neural.cz

  A blog about machine learning.

  Language:Makefile4405

• AADavin/RelativeDating

  Tools to date with transfers

  Language:Python3200

• Ecogenomics/basespace_project_downloader

  Download project fastq files from BaseSpace

  Language:Python3420

• evolbeginner/rrtc

  a script to do probability-based relaxed time constraint-based dating

  Language:Ruby2100