Pinned Repositories
coalescent-theory
NOT FREE SOFTWARE UNTIL AFTER MAY
convCal
Python scripts for calculation of expected number of convergence in Zou and Zhang 2015
Coursera-Bioinformatics
My solution to Bioinformatics Specialization (Finding Hidden Messages in DNA; Genome Sequencing; Comparing Genes, Proteins, and Genomes; Molecular Evolution; Genomic Data Science and Clustering; Finding Mutations in DNA and Proteins; Bioinformatics Capstone: Big Data in Biology)
GenomicPipelines
scripts writed during PHD
HMM
隐马尔科夫模型进行中文分词 python
MCMC
Collection of Monte Carlo (MC) and Markov Chain Monte Carlo (MCMC) algorithms applied on simple examples.
Positive_selection
Scripts for running codeml (from PAML package)
positiveSelectionPipeline
Random perl and shell scripts plus notes for whole genome CDS positive selection detection
prob140-textbook-zh
:book: [译] 面向数据科学的概率论
ThinkBayes
Code repository for Think Bayes.
BIGtigr's Repositories
BIGtigr/Positive_selection
Scripts for running codeml (from PAML package)
BIGtigr/positiveSelectionPipeline
Random perl and shell scripts plus notes for whole genome CDS positive selection detection
BIGtigr/codemlz
Modified version of codeml that can estimate eta under codon model.
BIGtigr/Discover_pseudogenes
Discover pseudogenes in a newly assembled genome, using reference gene/protein sequences.
BIGtigr/phylogenomics
(Mostly) Perl scripts that do something related to phylogenomic analysis.
BIGtigr/ThinkBayes
Code repository for Think Bayes.
BIGtigr/augustus
BIGtigr/bio-pipeline
My collection of light bioinformatics analysis pipelines for specific tasks
BIGtigr/biocode
Bioinformatics code libraries and scripts
BIGtigr/bioinformatics
Repository for student project
BIGtigr/GeneLossPipe
BIGtigr/GenomicPips
for genomic analysis
BIGtigr/methylome-tools
Tutorials for DNA methylome analysis tools
BIGtigr/N-furzeri-Genome-Analysis
BIGtigr/NGS
Scripts for next generation sequencing
BIGtigr/NGS_data_processing
Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.
BIGtigr/ngsutils
Tools for next-generation sequencing analysis
BIGtigr/nutvar2
Classifier of the potential pathogenicity of human genomic truncations
BIGtigr/omics
A Python package for omics data analysis
BIGtigr/paml-runner
Determines whether positive selection is acting on a gene.
BIGtigr/polysel
Pipeline to detect polygenic selection in gene sets
BIGtigr/positive-selection
Scripts and procedures for detecting positively selected genes and codons in primates
BIGtigr/psmc
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
BIGtigr/python-mle
A Python package for performing Maximum Likelihood Estimates
BIGtigr/pythonMisc
BIGtigr/Sample
BIGtigr/scripts_irb
BIGtigr/Shifted-Hamming-Distance
Source code for the Shifted Hamming Distance (SHD) filtering mechanism for sequence alignment. Described in the Bioinformatics journal paper (2015) by Xin et al. at http://users.ece.cmu.edu/~omutlu/pub/shifted-hamming-distance_bioinformatics15_proofs.pdf
BIGtigr/Smith-Waterman_viterbi
"Smith-Waterman alignment of two sequence, can be DNA or amino acids" "Also known as viterbi finding the maximum likelihood path of hidden states of a hidden Markov model (HMM)"
BIGtigr/stokepy
Stochastic models library for Python