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Adam Taranto

Login: Adamtaranto

Company: The Australian National University

Location: Canberra, Australia

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Repositories

2016-01-21-training-prep: null
bioconda-recipes: Conda recipes for the bioconda channel.
blast-besties: Rapid discovery of reciprocal best blast pairs.
catcount: Concatenate count tables for RNA-seq reads mapped to features by htseq-count
Corset-tools: Companion scripts for annotation of Corset generated transcript clusters.
density-Mapr: An R workflow for creating heat-maps representing the spatial association between two genomic feature sets
deRIP2: Predict progenitor sequence of fungal repeat families by correcting for RIP-like mutations and cytosine deamination events.
flo: Transfer annotations between genome assemblies using chained whole-genome alignment and UCSC LiftOver. Forked from wurmlab/flo.
frisk: Screen genomic scaffolds for regions of unusual k-mer composition.
gi2descript: Fetch summary data from NCBI for genbank records using GI numbers
hmmlearn: Hidden Markov Models in Python, with scikit-learn like API
HowToScience: A knowledge engine for new students of bioinformatics.
jcvi: Python utility libraries on genome assembly, annotation and comparative genomics
LTR-Harvest-Reformat: Correct sequence names in LTR_Harvest GFF3 output.
methFreq: Calculate observed vs expected instances of DNA-methylation motifs in gene sequences
mimeo: Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.
MITE_Hunter_2: Minor edits to allow MITE_Hunter (Han & Wessler 2010) to use modern blast+
mpg: Markovian sequence generator
nearestfeat: Fork of nearestfeat, a tool for calculating distance between members of feature classes in a GFF annotation. Migrating to Python3
promer2circos: Takes promer sequence matches formatted with show_coords, and reformats for use as a circos linkage track
pymummer: Python3 module for running MUMmer and reading the output
quick-ortho-fetch: Take an XML formatted multiblast result, extract genbank IDs for best x hits to each query and download a non-redundant list of matching seqs from ncbi.
RECONcile: Take clustered element fragment coordinates from RECON and write sequences to fasta for alignment and consensus calling.
Ribbon: Long read visualizer for genomics created using D3
sickle_team8: Giving a go at sickle
subset-fasta-by-name: Subset, split, and correct formatting of multiple sequence FASTA files.
SWC_ANU_2016: Python Stuff
TE-Annotation-Workflow: Workflow and useful tools for annotating transposable elements in sequenced genomes
TE-dispersion-metric: Proposed metric for measuring the clustering of transposons within a genome
TE-insertion-scanner: Scan whole genome alignments for signatures of transposon insertion.
TE-Reunite: For a set of reference transposons, collect instances from one or more genomes. Use aligned collections to build models capturing TE family diversity or produce deRIP'd reference sequence.
TE-splitter: Extract terminal repeats from retrotransposons (LTRs) or DNA transposons (TIRs). Compose synthetic MITES from complete DNA transposons.
TIRmite: Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.
Transposon-Tools-List: A list of useful software tools for predicting, classifying, annotating, and analysing Transposable Elements.
TRF2GFF: Convert Tandem Repeat Finder dat file output into gff3 format
Yanagiba: Filter and slice Nanopore reads which have been basecalled with Albacore.

Commits To

Repository	Most Recent Commit	# Commits
ISA-tools/bioconda-recipes	2017-10-24 18:11:29.0	4

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.