JosephLalli

JosephLalli's Stars

• joshpxyne/gpt-migrate

  Easily migrate your codebase from one framework or language to another.

  Language:Python6.9k5641493

• mre/idiomatic-rust

  🦀 A peer-reviewed collection of articles/talks/repos which teach concise, idiomatic Rust.

  Language:Rust6.9k16124213

• moshi4/pyCirclize

  Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

  Language:Python827104851

• owkin/PyDESeq2

  A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

  Language:Python6261114371

• j-andrews7/awesome-bioinformatics-benchmarks

  A curated and summarized list of bioinformatics bench-marking papers and resources.

  330184458

• jermp/data_compression_course

  A Crash Course on Data Compression.

  Language:C++3047224

• CompEpigen/figeno

  Tool for plotting sequencing data along genomic coordinates.

  Language:Python2596238

• lgmgeo/AnnotSV

  Annotation and Ranking of Structural Variation

  Language:Tcl2391026135

• jmschrei/tangermeme

  Biological sequence analysis for the modern age.

  Language:Python207102014

• marschall-lab/panacus

  Panacus is a tool for computing statistics for GFA-formatted pangenome graphs

  Language:Rust955478

• stephenslab/mashr

  An R package for multivariate adaptive shrinkage.

  Language:R911410719

• Illumina/PlatinumGenomes

  The Platinum Genomes Truthset

  8610159

• TileDB-Inc/TileDB-Vector-Search

  Cloud-native vector similarity search and storage with efficient, serverless scale-out

  Language:Jupyter Notebook55997

• schatzlab/crossstitch

  Code for phasing SVs with SNPs

  Language:Java528153

• lskatz/awesome-bioinformatics-jobs

  Resources for bioinformatics jobs

  49324

• at-cg/PanAligner

  Long read aligner for cyclic and acyclic pangenome graphs

  Language:C36454

• Midnighter/nextflow-gotchas

  A collection of unexpected challenges and learnings with nextflow and nf-core.

  Language:Shell34349

• asylvz/SVarp

  Phased structural variant discovery in pangenomes

  Language:C++32171

• srbehera/DRAGEN_Analysis

  Language:Python30154

• piquelab/QuASAR

  Quantitative Allele Specific Analysis of Reads. Joint genotyping & ASE inference for RNA-seq data

  Language:R2761110

• tkzeng/GeneBayes

  Language:Python24115

• COMBINE-lab/piscem

  Rust wrapper for the next generation (still currently in C++)

  Language:Rust238121

• fritzsedlazeck/nibSV

  Kmer based genotyper for short reads.

  Language:Nim23740

• gjun/muCNV

  Language:C++20264

• kcleal/SV_Benchmark_CMRG

  Structural variant benchmark of challenging medically relevant genes

  Language:Shell17201

• rwk-unil/sapphire

  Smart and Accurate Polishing of Phased Haplotypes Integrating Read Enhancements (SAPPHIRE)

  Language:C++10231

• bw2/ExpansionHunter

  A tool for estimating repeat sizes

  Language:C++7200

• ni-lab/CellTypeSpecificAccessibilityPrediction

  Language:Jupyter Notebook5101

• courtrun/HLA_finngen

  Language:R410

• pengkenlim/LSTrAP-denovo

  LSTrAP-denovo is an easy-to-use pipeline to assemble and annotate transcripts for species without genome / genomic annotations using publicly available RNA-seq data.

  Language:Python3211