Pinned Repositories
AD_POLB_ST
This repo contains the analysis scripts used in the paper Navarro et al. iScience, 2020. DOI:
awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
BioInfo_ML_courses
A bunch of python scripts and tools developed for BioInformatics and Machine Learning courses
hla_pipeline
DNA and RNA variant calling pipelines with HLA typing and Neoantigen predictions
Mingw-TokyoCabinet
My own implemenation of tokycabinet to make it compatible with WIN32/Mingw.
myVCF
MyVCF2: a web-based tool for the analysis and visualization of mutations stored in VCF files
Percolator-levelDB
My own implementation of leveldb to be integrated into Percolator.
st_analysis
A toolset for analysis and visualisation of Spatial Transcriptomics datasets.
st_pipeline
ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
st_viewer
A GUI tool for easy and smooth visualisation and analysis of Spatial Transcriptomics datasets
jfnavarro's Repositories
jfnavarro/st_pipeline
ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.
jfnavarro/st_analysis
A toolset for analysis and visualisation of Spatial Transcriptomics datasets.
jfnavarro/st_viewer
A GUI tool for easy and smooth visualisation and analysis of Spatial Transcriptomics datasets
jfnavarro/hla_pipeline
DNA and RNA variant calling pipelines with HLA typing and Neoantigen predictions
jfnavarro/myVCF
MyVCF2: a web-based tool for the analysis and visualization of mutations stored in VCF files
jfnavarro/scitron
jfnavarro/segment-anything
The repository provides code for running inference with the SegmentAnything Model (SAM), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.
jfnavarro/awesome-compbio-chatgpt
An awesome repository of community-curated applications of ChatGPT and other LLMs im computational biology
jfnavarro/batchglm
Fit generalized linear models in python.
jfnavarro/cellxgene
An interactive explorer for single-cell transcriptomics data
jfnavarro/cookiecutter-hypermodern-python
Hypermodern Python Cookiecutter
jfnavarro/CPA
The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.
jfnavarro/duplexseq
A pipeline to make consensus sequences from duplex sequencing
jfnavarro/geosketch
Geometry-preserving random sampling
jfnavarro/localstack
💻 A fully functional local AWS cloud stack. Develop and test your cloud & Serverless apps offline
jfnavarro/Makie.jl
High level plotting on the GPU.
jfnavarro/modern-unix
A collection of modern/faster/saner alternatives to common unix commands.
jfnavarro/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
jfnavarro/nf-tower
Nextflow Tower system
jfnavarro/pandera
A light-weight, flexible, and expressive statistical data testing library
jfnavarro/pixelator
A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.
jfnavarro/Plots.jl
Powerful convenience for Julia visualizations and data analysis
jfnavarro/pynguin
The PYthoN General UnIt Test geNerator is a test-generation tool for Python
jfnavarro/sarek
Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing
jfnavarro/scanorama
Panoramic stitching of single cell data
jfnavarro/scvi-tools
Deep probabilistic analysis of single-cell omics data
jfnavarro/seqlike
Unified biological sequence manipulation in Python
jfnavarro/spacemake
jfnavarro/stereoscope
Spatial mapping of cell types by integration of transcriptomics data
jfnavarro/tuplex
Tuplex is a parallel big data processing framework that runs data science pipelines written in Python at the speed of compiled code. Tuplex has similar Python APIs to Apache Spark or Dask, but rather than invoking the Python interpreter, Tuplex generates optimized LLVM bytecode for the given pipeline and input data set.