wdecoster

wdecoster's Stars

• snakemake/snakemake

  This is the development home of the workflow management system Snakemake. For general information, see

  Language:HTML2.3k561

• skovaka/UNCALLED

  Raw nanopore signal mapper that enables real-time targeted sequencing

  Language:C++52245

• BennyStrobes/SPOT

  SPlicing Outlier deTection

  Language:Python62

• BennyStrobes/Watershed

  Prioritization of functional rare genetic variants by integrating genomic annotations and RNA-seq

  Language:R1812

• llecompte/SVJedi

  SV genotyping with long reads

  Language:Python404

• tycho-kirchner/shournal

  Log shell-commands and used files. Snapshot executed scripts. Fully automatic.

  Language:C++1769

• csoneson/ExploreModelMatrix

  Explore design matrices interactively with R/Shiny

  Language:R362

• scottgigante/machine-learning-tutorial

  Machine learning tutorial for biologists, designed for Oz Single Cells 2019

  Language:Jupyter Notebook151

• nanoporetech/megalodon

  Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

  Language:Python19830

• isovic/raptor

  Graph-based mapping of long sequences, noisy or HiFi.

  Language:Perl542

• quinlan-lab/STRling

  Detect novel (and reference) STR expansions from short-read data

  Language:Nim639

• lh3/gfatools

  Tools for manipulating sequence graphs in the GFA and rGFA formats

  Language:C21621

• jvivian/gene-outlier-detection

  A Bayesian model for identifying gene expression outliers for individual single samples (N-of-1) when compared to a cohort of background datasets.

  Language:Python93

• lh3/minigraph

  Sequence-to-graph mapper and graph generator

  Language:C42338

• UCSC-nanopore-cgl/MarginPolish

  MarginPolish: Graph based assembly polishing

  Language:C469

• ENCODE-DCC/long-read-rna-pipeline

  ENCODE long read RNA-seq pipeline

  Language:wdl4413

• tpoorten/dotPlotly

  Generate an interactive dot plot from mummer or minimap alignments

  Language:HTML19356

• a-slide/NanopolishComp

  NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files

  Language:Python103

• chanzuckerberg/shasta

  [MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads

  Language:C++27259

• nhmkdev/cardmaker

  An application that generates graphics via data sources.

  Language:C#26141

• vgteam/vg

  tools for working with genome variation graphs

  Language:C++1.1k195

• cool-RR/PySnooper

  Never use print for debugging again

  Language:Python16.4k955

• bioinfomaticsCSU/deepsignal

  Detecting methylation using signal-level features from Nanopore sequencing reads

  Language:Python11221

• hasindu2008/f5c

  Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

  Language:C14826

• mikolmogorov/Flye

  De novo assembler for single molecule sequencing reads using repeat graphs

  Language:C797169

• brentp/slivar

  genetic variant expressions, annotation, and filtering for great good.

  Language:Nim25223

• pjedge/longshot

  diploid SNV caller for error-prone reads

  Language:Rust19426

• bwa-mem2/bwa-mem2

  The next version of bwa-mem

  Language:C++727102

• PacificBiosciences/pbsv

  pbsv - PacBio structural variant (SV) calling and analysis tools

  Language:Python13124

• DiltheyLab/HLA-LA

  Fast HLA type inference from whole-genome data

  Language:C++12941