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bio-utils

Bioinformatics utilities mostly written in Perl.

block-sampling

block sampling using modal values

classifying-bacteria-sequences

LSA 16SrRNA whole genome

coaxecva.github.io

codefights

codon-analysis

comp4030-design-and-analysis-of-algorithms

the course introduces fundamental algorithms design techniques such as divide and conquer, dynamic programming, greedy. Prerequisite: COMP 2700

comp7115-database-systems

[University of Memphis] Review of the relational model; query processing and optimization; physical database design and tuning; transaction processing; concurrency control; crash recovery; database buffer management; database security.

comp7150-fundamentals-of-data-science

The aim of this course is to introduce students to tools and techniques in all stages of the data science pipeline including, pre-processing, storage, visualization and analysis, in a domain-independent manner. The emphasis will be more on the practical aspects of data science. At the end of this course, students are expected to have the basic skills needed to start working in applications involving data science.

comp7295-bio-algorithm

Algorithms for problems arising in molecular biology, such as sequence matching, alignment, gene finding, sequence assembly, phylogeny, and structure prediction; internet resources; statistical analysis of DNA, RNA, and protein sequences

comp7712-algorithms-prob-solv

Covers algorithms problems, techniques, and design emphasizing problem solving and implementation skills; topics include advanced data structures, graph algorithms, string matching, network flow, dynamic programming, and randomized algorithms.

comp7745-machine-learning

An introduction to machine learning: hypothesis spaces, formation and evaluation; concept learning, decision trees, linear regression and perceptrons; graphical models (naive Bayes, Bayes Nets, Hidden Markov Models); computational learning theory; Support Vector Machines; instance-based learning

comp8780-natural-lang-processng

Computational aspects, algorithms, and techniques for human language processing; topics include lexical analysis, syntactic parsing, semantics, word sense disambiguation, logic forms, dialog, and pragmatics; applications include question answering and information extraction among others. PREREQUISITES: COMP 6040 or 6041 or permission of instructor.

data-science-analytics-in-python-workshop-uom-cs-dept

Dr. Vinhthuy Phan (instructor)

genbank-to-fasta

Fix to run with python3, originally from https://rocaplab.ocean.washington.edu/tools/genbank_to_fasta/

genome-assembly-complexity

Goal: get familiar with genome assemblers, pre-processing, reporting and validation.

graph

a simple graph module

hirschberg-implementation

linear space LCS

indel-analysis

Analysis of optimal alignments unfolds bias in existing variant profiles (BMC Bioinformatics 2016)

j2ee-tm-web-services

By Richard Monson-Haefel

lempel-ziv-complexity

LZ76 LZ78 Kolmogorov Complexity

longage

LongAGE: a memory-efficient implementation of Alignment with Gap Excision (AGE)

rna-seq-quantification

rcfmi, polyster, sudo-alignment

shannon-entropy

Compute Shannon entropy at length k for a genome (.fasta/.fa)

student-seat-arrangement

Arrange student seats in class for a test/exam

test_exe

for testing exe commit purposes

testing

Integrated Adaptive Resilient

unknown-bacteria-hunter

Using 16S rRNA Genes as Markers to Detect Unknown Bacteria in Microbial Communities (BMC Bioinformatics 2017)

ut-kbrin-r-workshop-2017

*12-1pm: Introduction to RStudio/R, Reading Data into R *1-2pm: Various data visualizations in R *2-3pm: Basic Statistical Analysis in R *3-3:45pm: Shiny Application Demo – Identifying Interaction Effects in Large Data Sets (shinyfsa.org) *3:45-5pm: Creation of a Shiny Application