Stephenda

Pinned Repositories

AdvancedHeatmapTutorial
for YouTube Channel
Language:R10
bcftools
This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib
Language:C00
breakdancer
SV detection from paired end reads mapping
Language:C++00
bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Language:C00
cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
Language:Perl0 1 00
code_snippets
Language:Jupyter Notebook00
dash
Analytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.
Language:Python00
delly
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Language:C++00
dfast_core
DDBJ Fast Annotation and Submission Tool
Language:Python00
hmmer
HMMER: biological sequence analysis using profile HMMs
Language:C10

Stephenda's Repositories

Stephenda/hmmer
HMMER: biological sequence analysis using profile HMMs
Language:C10
Stephenda/bcftools
This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib
Language:C00
Stephenda/bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Language:C00
Stephenda/cgview_comparison_tool
The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, and mitochondrial sequences.
Language:Perl0 1 00
Stephenda/code_snippets
Language:Jupyter Notebook00
Stephenda/dash
Analytical Web Apps for Python, R, Julia, and Jupyter. No JavaScript Required.
Language:Python00
Stephenda/delly
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
Language:C++00
Stephenda/dfast_core
DDBJ Fast Annotation and Submission Tool
Language:Python00
Stephenda/DiffLinker
DiffLinker: Equivariant 3D-Conditional Diffusion Model for Molecular Linker Design
Language:Python0 0
Stephenda/dotfiles
My dotfiles and personal preferences
Stephenda/FriPan
Interactive, web tool for exploring pan-genome of bacterial strains
Stephenda/gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Stephenda/KOALA-formatter
Script for converting raw KO-number output from GhostKOALA and BlastKOALA into hierarchically-structured CSV format
Stephenda/MesquiteCore
The core Mesquite repository
Stephenda/Nested-Pie-Chart
Nested Pie Chart in MatPlotLib for your dataset
Language:Jupyter Notebook1 0
Stephenda/new-git-test
Stephenda/OrthoFinder
Phylogenetic orthology inference for comparative genomics
Stephenda/orthologr
Genome wide orthology inference and dNdS estimation
Stephenda/phytools
Language:R1 0
Stephenda/plot_roary
plot_roary
Language:R1 0
Stephenda/plotly-tutorial
This Jupyter Notebook condenses the Plotly API into one easy to use document with examples
Stephenda/pseudofinder
Detection of pseudogene candidates in bacterial and archaeal genomes.
Stephenda/pyani
Python module for average nucleotide identity analyses
Stephenda/pygraphviz
Python interface to Graphviz graph drawing package
Stephenda/r4ds
R for data science: a book
Stephenda/RCandy
RCandy: an R package for visualising homologous recombination events in bacterial genomes
Stephenda/RNA-Seq
New user
Stephenda/rnabio.org
website for the rnaseq course
Stephenda/stephenda-
Repository
Language:HTML
Stephenda/WhatsGNU
WhatsGNU: a tool for identifying proteomic novelty