Pinned Repositories
ACCESS-Pipeline
cfDNA Sequencing Pipeline with UMI
ACCESS_SV_local
bio-playground
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
biopython
Official git repository for Biopython (converted from CVS)
cancer-genomics-workflow
MGI's CWL Cancer Pipelines.
CNApp
CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-friendly interface. The software uses segmented data from either aCGH, SNP-array, whole-exome sequencing or whole-genome sequencing to assess sample profiles and CNA levels, establishing associations with molecular and clinical features. CNApp has three main sections: Re-Seg & Score, Region profile and Classifier model
computer-science-flash-cards
Mini website for testing both general CS knowledge and enforce coding practice and common algorithm/data structure memorization.
concept-to-clinic
ALCF Concept to Clinic Challenge
covidclinicaldata
Coronavirus Disease 2019 (COVID-19) Clinical Data Repository
sv_annotator
andurill's Repositories
andurill/bio-playground
miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.
andurill/cancer-genomics-workflow
MGI's CWL Cancer Pipelines.
andurill/CNApp
CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-friendly interface. The software uses segmented data from either aCGH, SNP-array, whole-exome sequencing or whole-genome sequencing to assess sample profiles and CNA levels, establishing associations with molecular and clinical features. CNApp has three main sections: Re-Seg & Score, Region profile and Classifier model
andurill/concept-to-clinic
ALCF Concept to Clinic Challenge
andurill/DeepSVR
andurill/delly
DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
andurill/facets
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
andurill/gallery
Gallery of ggplot2 extensions
andurill/gameofthrones
Colour Palette for R inspired in the TV show Game of Thrones
andurill/hotspots
Identifying recurrent mutations in cancer
andurill/iCallSV
A Framework to call Structural Variants from NGS based datasets
andurill/maftools
:cancer: Summarize, Analyze and Visualize MAF files from TCGA or in house studies.
andurill/msisensor
microsatellite instability detection using paired tumor-normal
andurill/mutation_modelling
This repo has scripts that helps to generate features for modeling mutations
andurill/ngCGH
Tools for producing pseudo-cgh of next-generation sequencing data
andurill/noc-book
Repository for The Nature of Code book
andurill/nucleus
Python and C++ code for reading and writing genomics data.
andurill/oncoPrintr
R package to generate onco prints of genomic and clinical data of patient cohorts
andurill/pure
Pretty, minimal and fast ZSH prompt
andurill/pylearn2
Warning: This project does not have any current developer. See bellow.
andurill/pysamstats
A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
andurill/PyTorch-Tutorial
Build your neural network easy and fast
andurill/reveal.js
The HTML Presentation Framework
andurill/toil
A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
andurill/VarDict
VarDict
andurill/VarDictJava
VarDict Java port
andurill/vim-citylights
Vim port of City Lights colour scheme
andurill/waveforms
An interactive, explorable explanation about the peculiar magic of sound waves.
andurill/when-changed
Execute a command when a file is changed
andurill/z
z - jump around