Pinned Repositories
2020-Epigenetics_Workshop
ATAC-Seq, ChIP-Seq, and whole genome bisulfite! An introduction to analyzing some of the most popular types of epigenetic data.
agptools
Tools for working with agp files
AmpliconArchitect
AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon.
arriba
Fast and accurate gene fusion detection from RNA-Seq data
awesome-programming-books
📚 A curated list of awesome programming books (Algorithms and data structures, Artificial intelligence, Software Architecture, Human–computer interaction, Operating Systems, Database Systems, IT Security, Concurrency, Interpreters and Compilers, High-Performance Computing, Distributed Systems, Game Development, Mathematical optimization)
BINF511
bioinformatics-workbook
Bioinformatics Workbook repository
bioinfotools
Documenting usage and experience with bioinformatic tools
BioTutorials
Tutorial Notebooks of BioJulia
bisbee
alternative splicing analysis pipeline
mkyriak's Repositories
mkyriak/agptools
Tools for working with agp files
mkyriak/AmpliconArchitect
AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon.
mkyriak/arriba
Fast and accurate gene fusion detection from RNA-Seq data
mkyriak/CHORD
An R package for predicting HR deficiency from mutation contexts
mkyriak/cloneMap
An R package to plot maps of clone distributions in somatic evolution
mkyriak/clpipe
Python pipeline for neuroimaging data
mkyriak/DNA-seq-analysis
DNA sequencing analysis notes from Ming Tang
mkyriak/evo
DNA foundation modeling from molecular to genome scale
mkyriak/ggcoverage
Visualize and annotate genomic coverage with ggplot2
mkyriak/infercnv
Inferring CNV from Single-Cell RNA-Seq
mkyriak/long-read-pipelines
Long read production pipelines
mkyriak/Machine-learning-for-proteins
Listing of papers about machine learning for proteins.
mkyriak/maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
mkyriak/Mana
Command-line tool that analyses ONT alignments (.bam) to report quality control statistics
mkyriak/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
mkyriak/NanoCaller
Variant calling tool for long-read sequencing data
mkyriak/nanocomp
Comparison of multiple long read datasets
mkyriak/networkx
Network Analysis in Python
mkyriak/plotgardener
mkyriak/postcards
💌 Create simple, beautiful personal websites and landing pages using only R Markdown.
mkyriak/ribotin
mkyriak/rna-seq-pipeline
mkyriak/scarHRD
mkyriak/sigminer
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
mkyriak/spatialdata
An open and interoperable data framework for spatial omics data
mkyriak/speedseq
A flexible framework for rapid genome analysis and interpretation
mkyriak/training-collection
Collection of bioinformatics training materials
mkyriak/vechat
Correcting errors in noisy long reads using variation graphs
mkyriak/vistasoft
VISTASOFT is the main software repository of the VISTA lab at Stanford University.
mkyriak/wga-essentials
Docker image containing Whole Genome Assembly (WGA) essentials