walaj/svaba

Structural variation and indel detection by local assembly

Language: C++ - Size: 3.76 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 225 - Forks: 44

walaj/SeqLib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

Language: C++ - Size: 11.7 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 133 - Forks: 36

walaj/bwa Fork of lh3/bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

Language: C - Size: 1.64 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 2

walaj/fermi-lite Fork of lh3/fermi-lite

Standalone C library for assembling Illumina short reads in small regions

Language: C - Size: 298 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 1

walaj/cyftools

CLI tools for CyCIF

Language: C++ - Size: 1.18 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 2

walaj/bxtools

Tools for analyzing 10X Genomics data

Language: Makefile - Size: 144 KB - Last synced: 22 days ago - Pushed: over 5 years ago - Stars: 41 - Forks: 10

walaj/VariantBam

Filtering and profiling of next-generational sequencing data using region-specific rules

Language: Makefile - Size: 447 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 71 - Forks: 10

walaj/roverlaps

Fast and memory efficient genomic range overlaps for R

Language: C++ - Size: 702 KB - Last synced: 8 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0

walaj/varval

Rearrangement validation through targeted sequence realignment

Language: C++ - Size: 208 KB - Last synced: 8 months ago - Pushed: about 5 years ago - Stars: 3 - Forks: 0

walaj/KDTree Fork of crvs/KDTree

Simple C++ KD-Tree implementation

Language: C++ - Size: 21.5 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

walaj/walaj.github.io Fork of academicpages/academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

Language: JavaScript - Size: 47.6 MB - Last synced: 10 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 1

walaj/spatools-docs

Documentation for spatools

Size: 1000 Bytes - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

walaj/us-potus-model Fork of TheEconomist/us-potus-model

Code for a dynamic multilevel Bayesian model to predict US presidential elections. Written in R and Stan.

Size: 139 MB - Last synced: 10 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

walaj/SplitThreader Fork of MariaNattestad/SplitThreader

Explore rearrangements and copy-number amplifications in a cancer genome

Language: JavaScript - Size: 86.5 MB - Last synced: 10 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

walaj/SVsig Fork of ofershapira/SVsig

Recurrent structural variations detection in cancer whole genomes

Size: 6.49 MB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 1 - Forks: 1

walaj/svlib

Toolkit for extracting SVs from long sequences and benchmarking variant callers

Language: C++ - Size: 19.8 MB - Last synced: 10 months ago - Pushed: over 7 years ago - Stars: 13 - Forks: 2

walaj/spadf

Spatial biology data format

Language: C++ - Size: 85 KB - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

walaj/lattice Fork of broadinstitute/lattice

Size: 5.39 MB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

walaj/setup

Useful customizations of a unix environment

Language: Emacs Lisp - Size: 12.7 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

walaj/seqtools

Basic command-line sequence analysis utilities I can't find elsewhere

Language: C++ - Size: 10.7 KB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 2 - Forks: 0

walaj/pthread-lite

Light-weight header library for C++ concurrency with pthread

Language: C++ - Size: 11.7 KB - Last synced: 10 months ago - Pushed: over 7 years ago - Stars: 6 - Forks: 2

walaj/ncbitax2lin Fork of zyxue/ncbitax2lin

Convert NCBI taxonomy dump into lineages

Language: Python - Size: 253 KB - Last synced: 10 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

walaj/libtiff Fork of vadz/libtiff

OBSOLETE and not updated any more libtiff mirror, see website for the new one

Language: C - Size: 7.41 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

walaj/jUtils

R utilities and shortcuts

Language: R - Size: 1.95 KB - Last synced: 10 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

walaj/htslib Fork of samtools/htslib

C library for high-throughput sequencing data formats

Language: C - Size: 5.84 MB - Last synced: 10 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

walaj/gTrack Fork of mskilab-org/gTrack

R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework

Language: R - Size: 47.8 MB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

walaj/ginseng

Tools for 1D and 2D genomic significance analysis

Language: C++ - Size: 283 KB - Last synced: 10 months ago - Pushed: over 7 years ago - Stars: 2 - Forks: 0

walaj/freebayes Fork of freebayes/freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

Language: C++ - Size: 5.81 MB - Last synced: 10 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

walaj/ensapi

Command-line interface to Ensembl REST API

Language: C++ - Size: 2.93 KB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

walaj/encode-download

Download and process tracks from ENCODE

Language: Shell - Size: 2.93 KB - Last synced: 10 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 1

walaj/cycifr

R package for processing highly multiplexed spatial imaging data (e.g. CyCIF)

Language: Python - Size: 7.81 KB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

walaj/apophenia-clone

Copy of distribution version of Apophenia, with added statistical models

Language: Groff - Size: 2.12 MB - Last synced: 10 months ago - Pushed: over 7 years ago - Stars: 1 - Forks: 0

walaj/carreview

Manubot CAR-T Review Paper

Language: HTML - Size: 2.49 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

walaj/aws-cli-user-guide Fork of awsdocs/aws-cli-user-guide

The open source version of the AWS CLI User Guide

Size: 610 KB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

walaj/wips

Command line tools for image processing using libvips

Language: C++ - Size: 289 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

walaj/fishHook Fork of mskilab-org/fishHook

R package for applying Gamma-Poisson regression to identify statistical enrichment or depletion of somatic mutations in regions after correcting for genomic covariates.

Language: R - Size: 135 MB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0