Software

The Hallam Lab

Investigating microbial communities…

Software

HivePlotter

Visualizing large networks is tricky; conventional graph layout such as force directed layouts are inconsistent, often resemble "hair balls" and can even suggest patterns which aren't actually there. Then Martin Krzywinski (Genome Science Center, Vancouver, BC) developed 
hive plots, a coherent network layout algorithm that places nodes using predefined rules. Hive plots facilitate the visualization of structural patterns in a network and the comparison of networks.
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MetaPathways

MetaPathways is a modular pipeline for the integrated analysis of environmental sequence information, streamlining the analyses of many different projects across the Hallam lab. It takes an assembled or unassembled genomic sequence file (.fasta), predicts open reading frames (ORFs), and systematically produces a series of data products using the MEGAN, ML-TreeMap, tRNA-scan, and 16S SSU rRNA methods and softwares. The pipeline culminates in the production of an environmental pathway/genome database (ePGDB), inferring metabolic potential using the Pathway Tools software.
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fastLSA

Local Similarity Analysis (LSA) is a statistic used for detecting local and potentially lagged correlations. It differs from Pearson's Correlation Coefficient (PCC) by being sensitive to correlations that may not span the entire length of the time series, hence, LSA is sensitive to local correlations. Also, LSA can be allowed to be sensitive to lagged correlations, unlike PCC. LSA was not invented at the Hallam lab, but it was made efficient enough for the Hallam lab's data. Because older LSA software used random numbers to estimate statistical significance, it was too slow for practically sized data sets. We've developed fastLSA, a software package that uses an equation to calculate statistical significance, which is much faster.
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UBC Course Networks

The
UBC Course Networks website is a tool designed to help students navigate courses and help faculty examine the structure of their department. It uses information from the Student Service Centre to generate networks showing the prerequisite and corequisite relationships of UBC courses. The user can select any department or combination of departments to create a network on demand, then interact with it to rearrange the layout, modify the view, or see details for specific courses. The website relies on Python scripts for retrieving and storing the course information and for making this information into a network. It also uses the D3.js Javascript visualization library.
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Utilities

Bubble Charts (bubble.pl)
Have you ever wanted to draw a one or two-dimensional array of data as a figure in your manuscript? Historically, people have used a heatmap, with shades of color to indicate the value at each position in the array. The program described here uses black and white circles (bubbles) of different sizes to show the values.
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Fast Blast (fastblast.pl)
Have you ever wanted to extract a subset of BLAST results from a larger BLAST output file? Or extract a subset of sequences from a FASTA file? From examples found on the web, there is nothing available to do this in one step. This program provides a command-line method for doing both of these operations.
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GC Content (gccontent.pl)
Given an input .fasta file the script calculates the GC content of each of the entries.
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One Circos (onecircos.pl)
Given two input fasta sequences this script draws links, based on BLAST sequence simmilarity, using the Circos visualization software.
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BAM to FASTQ (bam2fastq.sh)
Converts BAM files to FASTQ files (created by Joshua Mell). Bedtools is the preferred software for this task, but bam2fastq.sh is valuable in its simplicity. Read the comments before using - it requires Samtools to run and does not produce the Casava 1.8-style FASTQ.
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