chazgoo Goto Github PK

2015

Public material for CS109

algaelgrowthanalysis

Final Project for CMSC 422 Spring 2020

bam-readcount

Count bases in BAM/CRAM files

bbmap

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

countclust

A R package for Grade of Membership model and Visualization of counts data:

ggfree

ggplot2-style plots with base R graphics

gsalign

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison

hcb_training-modules

Materials for short, half-day workshops

isa-analysis-pipeline

jbrowse

A modern genome browser built with JavaScript and HTML5.

jellyfish

A fast multi-threaded k-mer counter

jvarkit

Java utilities for Bioinformatics

kallisto

Near-optimal RNA-Seq quantification

library

Reference V, D, J, C genes

manta

Structural variant and indel caller for mapped sequencing data

misc_scripts

A collection of scripts I've used in various bioinformatic (and other) processes.

mysql-dimensions

Learning MySQL, building a structured database to organize various analyses from my (as yet unreleased) DIMENSIONS repository

oncovirus_tools

Suite of tools for the analysis of virus integration in cancer.

pysam

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

pysamstats

A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

repseqio

Utils for manipulations with RepSeq data. First step: utils to build V/D/J/C references.

samsa2

SAMSA pipeline, version 2.0. This version supports use on a local cluster using DIAMOND for annotations.

santa-sim

A forward-time simulator for gene sequences modeling a variety of mutation and selection processes.

sequence-manipulation

A range of different perl scripts for manipulating sequences, conducting alignments, consensus sequences, changing formats

shantou-2018

Syllabus and materials for the Summer 2018 algal genetics course held at University of Shantou

sleuth

Differential analysis of RNA-Seq

superseal

Reference guided viral quasispecies reconstruction

twt

Generic framework for the coalescent simulation of pathogen trees within host trees in R

viral-ngs

Viral genomics analysis pipelines

viral-vdap

Viral VDAP: a viral alignment, variant discovery, and annotation pipeline launched at the NCBI-Hackathon 2019