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brown-compbio

Tools developed in computational biology courses at Brown.

Each class has a folder containing multiple items

CSCI1820 - Algorithmic Foundations of Computational Biology

Sorin Istrail, Spring 2014

Homework 2

Repeated substring problem, repeated substrings with mismatches, dot plots implemented in python

Homework 3

Local alignment with inversions, finding contaminated segments within a sequence

Homework 4

Gene calling based on RNAseq density, constructing De Bruijn graphs from an input sequence

Homework 5

De Bruijn graph genome assembly and error correction

Homework 6

Midterm - Assembling contigs from an assembler into scaffolds

Homework 7

Viterbi algorithm for predicting CpG islands

Homework 8

BLAST implemented in python

PHP2620 - Statistical Methods in Bioinformatics 1

Jean Wu, Spring 2014

Homework 3

Differential expression analysis in classic estrogen microarray data and IFN-gamma / IL-1 beta treated thyroid epithelial cells.

BIOL1450 - Human Population Genomics

A simulation of coalescence times for genomics data

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