walaj

Oncology Fellow | Dana Farber Cancer Institute / Mass General Brigham

DFCIBoston, MA

Pinned Repositories

bxtools
Tools for analyzing 10X Genomics data
Language:Makefile41 7 2310
ginseng
Tools for 1D and 2D genomic significance analysis
Language:C++3 4 10
KDTree
Simple C++ KD-Tree implementation
Language:C++2 0 02
pthread-lite
Light-weight header library for C++ concurrency with pthread
Language:C++7 3 02
roverlaps
Fast and memory efficient genomic range overlaps for R
Language:C++3 3 10
SeqLib
C++ htslib/bwa-mem/fermi interface for interrogating sequence data
Language:C++133 19 4736
svaba
Structural variation and indel detection by local assembly
Language:C++227 17 13244
svlib
Toolkit for extracting SVs from long sequences and benchmarking variant callers
Language:C++13 3 02
VariantBam
Filtering and profiling of next-generational sequencing data using region-specific rules
Language:Makefile74 7 2210
varval
Rearrangement validation through targeted sequence realignment
Language:C++3 2 00

walaj's Repositories

walaj/svaba
Structural variation and indel detection by local assembly
Language:C++227 17 13244
walaj/SeqLib
C++ htslib/bwa-mem/fermi interface for interrogating sequence data
Language:C++133 19 4736
walaj/VariantBam
Filtering and profiling of next-generational sequencing data using region-specific rules
Language:Makefile74 7 2210
walaj/bxtools
Tools for analyzing 10X Genomics data
Language:Makefile41 7 2310
walaj/ginseng
Tools for 1D and 2D genomic significance analysis
Language:C++3 4 10
walaj/roverlaps
Fast and memory efficient genomic range overlaps for R
Language:C++3 3 10
walaj/varval
Rearrangement validation through targeted sequence realignment
Language:C++3 2 00
walaj/KDTree
Simple C++ KD-Tree implementation
Language:C++2 0 02
walaj/seqtools
Basic command-line sequence analysis utilities I can't find elsewhere
Language:C++2 2 00
walaj/fermi-lite
Standalone C library for assembling Illumina short reads in small regions
Language:C1 2 01
walaj/setup
Useful customizations of a unix environment
Language:Emacs Lisp1 2 0
walaj/SVsig
Recurrent structural variations detection in cancer whole genomes
Language:MATLAB1 2 01
walaj/aws-cli-user-guide
The open source version of the AWS CLI User Guide
1 0
walaj/bwa
Burrow-Wheeler Aligner for pairwise alignment between DNA sequences
Language:C2 02
walaj/carreview
Manubot CAR-T Review Paper
Language:HTML1 0
walaj/cycifr
R package for processing highly multiplexed spatial imaging data (e.g. CyCIF)
Language:Python1 0
walaj/cyftools
CLI tools for CyCIF
Language:C++1 02
walaj/cyslib
C library for high-throughput multiplex imaging data formats
Language:C0 0
walaj/cytif
Command line tools for image processing using libvips
Language:C++2 0
walaj/ensapi
Command-line interface to Ensembl REST API
Language:C++2 0
walaj/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:R2 0
walaj/freebayes
Bayesian haplotype-based polymorphism discovery and genotyping.
Language:C++2 0
walaj/gTrack
R package for visualizing complex and multi-track 1D and 2D genomic data in GenomicRanges framework
Language:R2 0
walaj/jUtils
R utilities and shortcuts
Language:R2 0
walaj/lattice
walaj/libtiff
OBSOLETE and not updated any more libtiff mirror, see website for the new one
Language:C0 0
walaj/ncbitax2lin
Convert NCBI taxonomy dump into lineages
Language:Python2 0
walaj/SplitThreader
Explore rearrangements and copy-number amplifications in a cancer genome
Language:JavaScript2 0
walaj/us-potus-model
Code for a dynamic multilevel Bayesian model to predict US presidential elections. Written in R and Stan.
Language:HTML1 0
walaj/walaj.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
Language:JavaScript2 01