Pinned Repositories
picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
prymer
Python Primer Design Library
covid_rna_splicing
pairix
1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates
permutect
Mutect3
yfarjoun's Repositories
yfarjoun/permutect
Mutect3
yfarjoun/aFC
Calculates allelic Fold Change (aFC) using standard input files for fastQTL.
yfarjoun/bustools
Tools for working with BUS files
yfarjoun/biopython
Official git repository for Biopython (originally converted from CVS)
yfarjoun/CellBender
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
yfarjoun/ddqc
Biology-centered data-driven quality control for scRNA-seq
yfarjoun/docker-cellranger
Dockerized Cell Ranger
yfarjoun/EagleC
A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
yfarjoun/fastqtl
Enhanced version of the FastQTL QTL mapper
yfarjoun/featured-notebooks
yfarjoun/fgbio
Tools for working with genomic and high throughput sequencing data.
yfarjoun/fgprimer
APIs and wrappers for performing PCR primer design related tasks
yfarjoun/gcodeplot
Use a 3-axis machine as a pen plotter
yfarjoun/gwas-summary-statistics-standard
Documentation on new GWAS Summary Statistics Standard
yfarjoun/hgvs-parser
HGVS variant description parser
yfarjoun/horsefish
yfarjoun/hts-specs
Specifications of SAM/BAM and related high-throughput sequencing file formats
yfarjoun/kb_python
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
yfarjoun/magrittr
Improve the readability of R code with the pipe
yfarjoun/nextflow
A DSL for data-driven computational pipelines
yfarjoun/palantir-workflows-test1
Utility workflows for the DSP palantir team
yfarjoun/picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
yfarjoun/poetry
Python packaging and dependency management made easy
yfarjoun/pyranges
Performant Pythonic GenomicRanges
yfarjoun/scanpy
Single-cell analysis in Python. Scales to >1M cells.
yfarjoun/seqtk
Toolkit for processing sequences in FASTA/Q formats
yfarjoun/stitch
Stitch is a toolkit for analysis of chimeric reads in sequencing data
yfarjoun/terra-notebook-utils
Utilities for the Terra notebook environment.
yfarjoun/VerifyBamID
VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
yfarjoun/warp
WDL Analysis Research Pipelines