Open source software
- concordex: Quantitative assessment of single-cell RNA-seq clustering (Python)
- concordexR: Quantitative assessment of single-cell RNA-seq clustering (R)
- ffq: Find sequencing data and metadata from public databases
- gget: Efficient querying of genomic reference databases
- k-spaces: Fit mixtures of low dimensional Gaussian latent variable models for data modeling, dimension reduction, and subspace learning
- kallisto: Pseudoalignment for mapping sequence reads to targets, including quantification bulk and single-cell RNA-seq data
- kb-python: Wrapper for the kallisto | bustools workflow for single-cell RNA-seq preprocessing
- kite: Fast and accurate preprocessing of feature barcode experiments
- metakallisto: metagenomics analysis with kallisto
- monod: Fit chemical master equation models to sequencing data
- PCCA: Couple PCA to CCA
- rhoPCA: The ρPCA method for contrastive PCA of single-cell RNA-seq data
- seqspec: A machine-readable YAML file format for genomic library sequence and structure
- SpatialFeatureExperiment: Extension of SpatialExperiment with sf
- sleuth: Differential analysis of bulk RNA-seq
- splitcode: Flexible and efficient preprocessing, parsing, and manipulation of sequencing reads
- qcbc: Quality control synthetic barcode sequences for orthogonal sequencing-based assays
- voyager: Platform for exploratory spatial single-cell genomics data analysis
- wompwomp: Make alluvial plots with node order and colors optimized to minimize edge crossings
Open source hardware
Article repositories
These repositories contain code to reproduce figures and results from papers. Each repository has the naming convention [initials of author last names in order of appearance in the article]_[year published].
- CJP_2025
- SBRGKLAYWMP_2025
- RLSRP_2025
- OP_2025
- SBP_2025
- KP_2025
- FP_2025
- ROP_2025
- FCSKPP_2025
- SHSOHMP_2024
- MHRP_2024
- FLP_2024
- MEPSP_2024
- LSRRSRLFKOTWMWMP_2024
- LP_2024
- CGP_2024_2
- RMEJLBASBMP_2024
- HCP_2024
- GBP_2024
- BGP_2024
- HSSHMP_2024
- FGP_2024
- LSCHWCP_2023
- CP_2023
- CGCCP_2023
- GVP_2023
- GP_2023
- BGP_2023
- JBMMCKP_2023
- CGP_2023
- BSP_2023
- DBALLSMRDMCMGWSTPMBDKPFP_2023
- KBP_2023
- GFCP_2022
- CBP_2022
- BHGP_2022
- GYP_2022
- BP_2022
- GCCP_2022
- HSHMP_2022
- HPM_2022
- CWGFLHGCCHAP_2021
- GP_2021
- GVFP_2021
- CP_2021
- MBLGLMBHGP_2021
- LP_2021
- BP_2021
- BKMGP_2021
- CBP_2021
- BYVSTZP_2020
- GP_2020
- BP_2020
- BLCSBGLKP_2020
- GRNP_2020
- BTRBP_2020
- BMGP_2020
- GSP_2019
- MBGBLHGP_2019
- SP_2019
- SBP_2019
- GPCTP_2019
- SGYP_2019
- NYMP_2018
- PM_2018
- YLMP_2018