Pinned Repositories
amatch
Approximate String Matching library
biopython
My fork of the official Biopython repository, used for experimental branches etc
bioruby
bioruby
bioruby-biolinux
Meta package for BioLinux distribution
bioruby-faster
A fast and simple parser for Fasta / FastQ files
bioruby-gem
BioGem helps Bioinformaticians start developing plugins/modules for BioRuby creating a scaffold and a gem package
bioruby-ngs
This plugins is intended to wrap the common software used for Next Generation Sequencing data
bioruby-plugin-graphics
Bio::Graphics is a ruby library for visualizing annotations on chromosomes
bioruby-ucsc-api
Ruby UCSC API: An API for the UCSC Genome Database
Cytoscape_Course
This is a basic cytoscape course intended for beginners to get training with biological network analysis.
a1aks's Repositories
a1aks/peptides
a1aks/kallisto
Near-optimal RNA-Seq quantification
a1aks/gatk3-4-rnaseq-germline-snps-indels
Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools
a1aks/u24_lymphocyte
a1aks/XenoSplit
Mapping pipeline
a1aks/decoder
Matlab repository for DECODER
a1aks/Metagenomic-Disease-Classification-With-Deep-Learning
This repository accompanies the paper "Multiclass Disease Classification from Microbial Whole-CommunityMetagenomes using Graph Convolutional Neural Networks."
a1aks/cytoscape-tutorials
Collection of modular Cytoscape tutorials for online presentation using reveal.js
a1aks/vcflib
a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
a1aks/biocluster
Tutorial on building a computing cluster for bioinformatics
a1aks/NMF
NMF: A Flexible R package for Nonnegative Matrix Factorization
a1aks/OptiType
Precision HLA typing from next-generation sequencing data
a1aks/STAR
RNA-seq aligner
a1aks/d3
Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:
a1aks/delly
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
a1aks/pandas
Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
a1aks/PRECISE
a1aks/PRECISE_figures
Jupyter notebooks and code to reproduce figures
a1aks/combat.py
python / numpy / pandas / patsy version of ComBat for removing batch effects.
a1aks/resources
a1aks/IIT_proteogenomics_workshop
Hands-on for IIT workshop
a1aks/RCy3
New version of RCy3, redesigned and collaboratively maintained by Cytoscape developer community
a1aks/protigy
Proteomics Toolset for Integrative Data Analysis
a1aks/population-gcn
Graph CNNs for population graphs
a1aks/scRNA.seq.course
Analysis of single cell RNA-seq data course
a1aks/rnaseq_tutorial
Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.
a1aks/netMHCpan-4.0-parse
Parses xls files created by netMHCpan-4.0
a1aks/PhISCS
Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data
a1aks/MSstats
R package - MSstats
a1aks/BBMap
(Not Offical) BBMap short read aligner, and other bioinformatic tools.