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Projects in Awesome Lists by sjackman

A curated list of projects in awesome lists by sjackman .

https://github.com/sjackman/lambdar

ƛR: Run R on AWS Lambda

Last synced: 21 Nov 2024

https://github.com/sjackman/fastascripts

Manipulate FASTA files

Last synced: 12 Oct 2024

https://github.com/sjackman/uniqtag

Abbreviate strings to short, unique identifiers

Last synced: 28 Oct 2024

https://github.com/sjackman/docker-bio

Docker images of bioinformatics software

Last synced: 21 Nov 2024

https://github.com/sjackman/makefile-example

An example of a data analysis pipeline using Make

Last synced: 21 Nov 2024

https://github.com/sjackman/assembly-graph

Compare assembly graph file formats

Last synced: 21 Nov 2024

https://github.com/sjackman/docker-linuxbrew

:skull: Defunct. Use https://github.com/Linuxbrew/docker

Last synced: 21 Nov 2024

https://github.com/sjackman/uniqtag-paper

UniqTag: Content-derived unique and stable identifiers for gene annotation

Last synced: 21 Nov 2024

https://github.com/sjackman/open-science

:microscope: Open, reproducible science using Make, RMarkdown and Pandoc

markdown open-science reproducible-science slides

Last synced: 12 Oct 2024

https://github.com/sjackman/gfalint

Check a GFA file for syntax errors

Last synced: 21 Nov 2024

https://github.com/sjackman/abyss-scaffold-paper

Scaffolding a genome sequence assembly using ABySS

Last synced: 21 Nov 2024

https://github.com/sjackman/picea-glauca-mitochondrion

Mitochondrial genome of white spruce (Picea glauca)

Last synced: 21 Nov 2024

https://github.com/sjackman/homebrewr

An R package to install software using Homebrew

Last synced: 12 Oct 2024

https://github.com/sjackman/abyss-activity

ABySS learning activity

Last synced: 21 Nov 2024

https://github.com/sjackman/fastgtools

Tools to manipulate FASTG files

Last synced: 21 Nov 2024

https://github.com/sjackman/white-spruce-organelles-paper

:evergreen_tree: Organellar Genomes of White Spruce (Picea glauca)

Last synced: 21 Nov 2024

https://github.com/sjackman/minitig

Assemble short reads into contigs using minimizers

Last synced: 21 Nov 2024

https://github.com/sjackman/picea-sitchensis-mitochondrion

🧬🌲 Mitochondrial genome of Sitka spruce (Picea sitchensis)

Last synced: 21 Nov 2024

https://github.com/sjackman/resume

PhD graduate in bioinformatics, programmer, engineer

resume

Last synced: 21 Nov 2024

https://github.com/sjackman/samskrit

Tools to manipulate SAM and BAM files

Last synced: 21 Nov 2024

https://github.com/sjackman/dotfiles

~/.*

dotfiles

Last synced: 12 Oct 2024

https://github.com/sjackman/picea-sitchensis-mitochondrion-paper

🧬🌲 Largest Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates Complex Physical Structure

Last synced: 21 Nov 2024

https://github.com/sjackman/linuxbrew-slides

Linuxbrew and Homebrew-Science

Last synced: 21 Nov 2024

https://github.com/sjackman/abyss-drosophila-melanogaster

:microscope: Assemble Drosophila melanogaster with ABySS

abyss assembly drosophila genome

Last synced: 21 Nov 2024

https://github.com/sjackman/thesis

PhD Thesis: Efficient Assembly of Large Genomes

bioinformatics genomics

Last synced: 21 Nov 2024

https://github.com/sjackman/linkage-map-slides

Scaffolding genome sequence assemblies using a linkage map

presentation slides

Last synced: 21 Nov 2024

https://github.com/sjackman/talr

TALR: Targeted Assembly of Linked Reads

Last synced: 21 Nov 2024

https://github.com/sjackman/mars-rover

:rocket: Extraterrestrial DNA! :rocket:

Last synced: 21 Nov 2024

https://github.com/sjackman/makefile-slides

:microscope: Automating Data Analysis Pipelines

Last synced: 21 Nov 2024

https://github.com/sjackman/abyss-pipeline

Scaling ABySS to longer reads using spaced k-mers and Bloom filters

Last synced: 21 Nov 2024

https://github.com/sjackman/distance-estimator-paper

Estimate the distance between two nucleotide sequence fragments using paired-end reads

Last synced: 21 Nov 2024

https://github.com/sjackman/stat540-project

STAT 540 group project

Last synced: 21 Nov 2024

https://github.com/sjackman/ogdraw

A mirror of OrganellarGenomeDRAW

Last synced: 21 Nov 2024

https://github.com/sjackman/thesis-committee

PhD thesis committee presentation slides

Last synced: 21 Nov 2024

https://github.com/sjackman/tigmint-data

Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules

10xgenomics bioinformatics bioinformatics-analysis genome-assembly genome-scaffolding linked-reads misassembly-correction

Last synced: 21 Nov 2024

https://github.com/sjackman/picea-sitchensis-mitochondrion-legacy

:evergreen_tree: Mitochondrial genome of Sitka spruce (Picea sitchensis)

Last synced: 21 Nov 2024

https://github.com/sjackman/linuxbrew-paper

:beer::penguin: Linuxbrew Enables Repeatable Cross-Platform Scientific Software Installation

Last synced: 21 Nov 2024

https://github.com/sjackman/assembly-slides

Genome sequence assembly slides

Last synced: 21 Nov 2024

https://github.com/sjackman/marmot-mitochondrion

Yellow-bellied marmot

genome-assembly

Last synced: 21 Nov 2024

https://github.com/sjackman/konnector-vis

Visualize an ABySS-Konnector graph

Last synced: 21 Nov 2024

https://github.com/sjackman/picea-sitchensis-organelles-poster

:evergreen_tree: Organellar Genomes of Sitka Spruce (Picea sitchensis): Assembly and Annotation

Last synced: 21 Nov 2024

https://github.com/sjackman/sjackman.github.io

The personal web site of Shaun Jackman

bioinformatics genome-assembly science

Last synced: 21 Nov 2024

https://github.com/sjackman/snoove

Create a dendrogram from genome sequencing data

Last synced: 21 Nov 2024

https://github.com/sjackman/rewrite-git-history

Rewrite the history of a git fork to match the history of its parent

Last synced: 21 Nov 2024

https://github.com/sjackman/picea-sitchensis-organelles-slides

:evergreen_tree: Organellar Genomes of Sitka Spruce (Picea sitchensis): 
Assembly and Annotation

Last synced: 21 Nov 2024

https://github.com/sjackman/10xgenomics-slides

Efficient Assembly of Large Genomes

Last synced: 21 Nov 2024

https://github.com/sjackman/scaffolding-coverage

Determine the required mate-pair coverage for scaffolding

Last synced: 21 Nov 2024

https://github.com/sjackman/gfa2-slides

:microscope: Graphical Fragment Assembly (GFA) 2.0

Last synced: 21 Nov 2024

https://github.com/sjackman/playground

A playground for experimentation

Last synced: 21 Nov 2024

https://github.com/sjackman/tupper

Tupper's self-referential formula

Last synced: 21 Nov 2024

https://github.com/sjackman/wiki

My notes

Last synced: 21 Nov 2024

https://github.com/sjackman/tigmint-paper

Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules

10xgenomics bioinformatics genome-assembly genome-scaffolding linked-reads manuscript misassembly-correction

Last synced: 21 Nov 2024

https://github.com/sjackman/giab-slides

Assembling the Genome in a Bottle sequencing data with ABySS

Last synced: 21 Nov 2024

https://github.com/sjackman/rosalind

Rosalind solutions in Haskell

Last synced: 21 Nov 2024

https://github.com/sjackman/abyss-bloom-fpr

Effect of Bloom filter false positive rate on assembly with ABySS

Last synced: 21 Nov 2024

https://github.com/sjackman/pgcpdna-wgs-assembly

:evergreen_tree: Analyze plastid DNA (cpDNA) of white spruce (Picea glauca)

Last synced: 21 Nov 2024

https://github.com/sjackman/pgcpdna

:evergreen_tree: Annotate the plastid genome of white spruce (Picea glauca)

Last synced: 21 Nov 2024

https://github.com/sjackman/picea-glauca-organelles

:evergreen_tree: Align linked reads to the white spruce organelles

Last synced: 21 Nov 2024

https://github.com/sjackman/homebrew-tap

Personal formulae for the Homebrew package manager

Last synced: 21 Nov 2024

https://github.com/sjackman/abyss2-slides

ABySS 2.0: Resource-efficient assembly of large genomes using a Bloom filter

Last synced: 21 Nov 2024

https://github.com/sjackman/cpsc540-project

CPSC 540 Term Project

Last synced: 21 Nov 2024

https://github.com/sjackman/abstracts

Conference abstracts

Last synced: 21 Nov 2024

https://github.com/sjackman/makefile-example-stat545

Makefile example for STAT 545

Last synced: 21 Nov 2024

https://github.com/sjackman/uniqtag-slides

UniqTag: Content-derived unique and stable identifiers for gene annotation

Last synced: 21 Nov 2024

https://github.com/sjackman/uniqtag-data

Supplementary data for the UniqTag paper

Last synced: 21 Nov 2024

https://github.com/sjackman/review-regionreport

Review of regionReport

Last synced: 21 Nov 2024

https://github.com/sjackman/tabtools

Scripts to manipulate tab-delimited data

Last synced: 21 Nov 2024

https://github.com/sjackman/large-molecule-slides

:microscope: Assembling Genomes Using Large Molecule Sequencing

Last synced: 21 Nov 2024

https://github.com/sjackman/linuxbrew-core

:beers::penguin: Core formulae for the Linuxbrew package manager

Last synced: 16 Dec 2024

https://github.com/sjackman/psitchensismt-slides

Mitochondrial Genome of Sitka Spruce (Picea sitchensis)

Last synced: 21 Nov 2024

https://github.com/sjackman/homebrew-linux-dev

:wrench::penguin: Tools for Linuxbrew developers

Last synced: 21 Nov 2024

https://github.com/sjackman/tigmint-slides

Tigmint: Correct Misassemblies Using Linked Reads From Large Molecules

10x abyss assembly chromium genome gymnosperm linked-reads misassembly-correction mitochondrion scaffolding

Last synced: 21 Nov 2024

https://github.com/sjackman/tigmint-recomb-slides

Tigmint: Correcting Misassemblies Using Linked Reads From Large Molecules

Last synced: 21 Nov 2024

https://github.com/sjackman/picea-sitchensis-plastid

:evergreen_tree: Annotate the plastid genome of Sitka spruce (Picea sitchensis)

Last synced: 21 Nov 2024

https://github.com/sjackman/pg-odna-transfer

:evergreen_tree: Analyze organellar DNA transfer in white spruce (Picea glauca)

Last synced: 21 Nov 2024