kmsouthard

kmsouthard's Stars

• emdann/milopy

  Python implementation of Milo for differential abundance testing on KNN graph

  Language:Jupyter Notebook556

• ponnhide/pyCircos

  python Circos

  Language:Python31866

• moshi4/pyCirclize

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

  Language:Python66640

• jeffhussmann/hits

  utilities for processing high-throughput sequencing experiments

  Language:HTML44

• gaolabtools/scNanoGPS

  Single cell Nanopore sequencing data for Genotype and Phenotype

  Language:Python341

• epi2me-labs/wf-single-cell

  Language:Python6429

• Sun-lab/ideas

  Individual level Differential Expression Analysis for Single cells

  Language:R224

• mqzhanglab/BSDE

  A single-cell RNAseq differential expression analysis approach in case-control study

  Language:R71

• pachterlab/seqspec

  machine-readable file format for genomic library sequence and structure

  Language:Python10617

• sridnona/cb_sniffer

  mutation(barcode) caller for 10x single cell data

  Language:Python4116

• pachterlab/GFCP_2022

  RNA velocity validation

  Language:Jupyter Notebook231

• ventolab/CellphoneDB

  CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.

  Language:Jupyter Notebook30751

• google-deepmind/alphafold

  Open source code for AlphaFold.

  Language:Python12.1k2.2k

• klarman-cell-observatory/Perturb-CITE-seq

  Language:Python142

• cookiecutter/cookiecutter

  A cross-platform command-line utility that creates projects from cookiecutters (project templates), e.g. Python package projects, C projects.

  Language:Python22k2k

• MaayanLab/clustergrammer

  An interactive heatmap visualization built using D3.js

  Language:JavaScript23086

• gao-lab/Cell_BLAST

  A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.

  Language:Python8212

• seandavi/awesome-single-cell

  Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

  3k941

• COMBINE-lab/salmon

  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

  Language:C++748159

• COMBINE-lab/alevin-fry

  🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

  Language:Rust15615

• josephreplogle/target_enrichment

  Tools for empirical design of hybridization-based target enrichment probes for 3' single-cell RNA-seq

  Language:Jupyter Notebook51

• josephreplogle/guide_calling

  Tools for sgRNA calling in direct capture Perturb-seq data

  Language:Python264

• swcarpentry/swcarpentry

  A meta-repository to help navigate the many lessons and repos of the Software Carpentry Community

  568105

• swcarpentry/v4

  Software Carpentry Version 4 lessons.

  Language:HTML3312

• brianhie/scanorama

  Panoramic stitching of single cell data

  Language:Python25346

• Phlya/adjustText

  A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps.

  Language:Jupyter Notebook1.5k87

• YosefLab/Cassiopeia

  A Package for Cas9-Enabled Single Cell Lineage Tracing Tree Reconstruction

  Language:Python7424

• scverse/scvi-tools

  Deep probabilistic analysis of single-cell and spatial omics data

  Language:Python1.2k341

• scikit-bio/scikit-bio

  scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

  Language:Python865270

• hbctraining/DGE_workshop

  Language:HTML360165