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
- 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
- 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
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].
- 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