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A list of software, databases, websites, and other projects that I’ve created or made significant contributions to.
| Name | Title | Authors | GitHub | Link | PaperLink | Released | OpenSource | Language | Type | Distribution |
|---|---|---|---|---|---|---|---|---|---|---|
| autoCV | Automatically generate and style your CV from tables. | BM Schilder | https://github.com/bschilder/autoCV | TRUE | TRUE | R, HTML, CSS, JavaScript | package | GitHub | ||
| anndataR | Bring the power and flexibility of AnnData to the R ecosystem, allowing you to effortlessly manipulate and analyze your single-cell data. | R Cannoodt, L Zappia, M Morgan, L Deconinck, D Bredikhin, I Virshup, BM Schilder, C Sang-aram | https://github.com/scverse/anndataR | TRUE | TRUE | R, Python | package | GitHub | ||
| gptPhD | Query Large Language Models for the purposes of systematically extracting biomedical knowledge. | BM Schilder, KB Murphy, NG Skene | https://github.com/neurogenomics/gptPhD | FALSE | TRUE | R | package | GitHub | ||
| ThreeWayTest | Summary statistics-based association test for identifying the pleiotropic effects with set of genetic variants | D Bu, BM Schilder | https://github.com/bschilder/ThreeWayTest | TRUE | TRUE | R | package | GitHub | ||
| SCAVENGE | Variant to function mapping at single-cell resolution through network propagation | F Yu, BM Schilder | https://github.com/sankaranlab/SCAVENGE | https://doi.org/10.1038/s41587-022-01341-y | TRUE | TRUE | R | package | GitHub | |
| rworkflows | Continuous integration for R packages. Automates testing, documentation website building, and containerised deployment | BM Schilder, AE Murphy, NG Skene | https://github.com/neurogenomics/rworkflows | https://doi.org/10.21203/rs.3.rs-2399015/v1 | TRUE | TRUE | R, Python | package | GitHub | |
| TIPseeker | R package for post-processing [single-cell] TIP-seq data | BM Schilder, T Ronkko, NG Skene | https://github.com/neurogenomics/TIPseeker | FALSE | FALSE | R | package | GitHub | ||
| PeakyFinders | R package for mining, calling, and importing epigenomic peaks | BM Schilder, NG Skene | https://github.com/neurogenomics/PeakyFinders | FALSE | FALSE | R | package | GitHub | ||
| graphiti | Extract colour palettes from graffiti artworks. | BM Schilder | https://github.com/bschilder/graphiti | FALSE | TRUE | R | package | GitHub | ||
| SkillNet | Creates user-specific contribution networks from GitHub Organization repositories | BM Schilder | https://github.com/neurogenomics/SkillNet | TRUE | TRUE | R | package | GitHub | ||
| phenoRx | Make cell type-specific predictions for patients based on clinical phenotypes and/or risk genes. | BM Schilder | https://github.com/neurogenomics/phenoRx | FALSE | TRUE | R | package | GitHub | ||
| phenomix | R package for the exploration and analysis of many genotype-phenotype datasets at once | BM Schilder | https://github.com/neurogenomics/phenomix | FALSE | TRUE | R, Python | package | GitHub | ||
| MAGMA_Celltyping | Identify cell types underlying the associations found in GWAS summary statistics | BM Schilder, AE Murphy, J Bryois, NG Skene | https://github.com/neurogenomics/MAGMA_Celltyping | TRUE | TRUE | R | package | GitHub | ||
| EWCE | Expression Weighted Celltype Enrichment | AE Murphy, BM Schilder, NG Skene | https://github.com/NathanSkene/EWCE | TRUE | TRUE | R | package | Bioconductor | ||
| EpiArchives | Public archive for EpiCompare reports. | BM Schilder, S Choi | https://github.com/neurogenomics/EpiArchives | https://doi.org/10.1101/2022.07.22.501149 | TRUE | TRUE | R | database | GitHub | |
| EpiCompare | R package for QC and benchmarking epigenetic datasets | S Choi, BM Schilder, L Abbasova, AE Murphy, NG Skene | https://github.com/neurogenomics/EpiCompare | https://doi.org/10.1101/2022.07.22.501149 | TRUE | TRUE | R | package | Bioconductor | |
| MultiEWCE | R package for analysing multiple gene lists using EWCE | BM Schilder, B Gordon-Smith, NG Skene | https://github.com/neurogenomics/MultiEWCE | https://doi.org/10.1101/2023.02.13.23285820 | TRUE | TRUE | R | package | GitHub | |
| HPOExplorer | Functions for working with the Human Phenotype Ontology data | B Gordon-Smith, BM Schilder, NG Skene | https://github.com/neurogenomics/HPOExplorer | https://doi.org/10.1101/2023.02.13.23285820 | TRUE | TRUE | R | package | GitHub | |
| orthogene | Interspecies gene mapping | BM Schilder, NG Skene | https://github.com/neurogenomics/orthogene | TRUE | TRUE | R | package | Bioconductor | ||
| MungeSumstats | Standardise the format of summary statistics from GWAS | AE Murphy, BM Schilder, NG Skene | https://github.com/neurogenomics/MungeSumstats | https://doi.org/10.1093/bioinformatics/btab665 | TRUE | TRUE | R | package | Bioconductor | |
| scNLP | Tools for applying natural language processing (NLP) techniques to single-cell (sc) omics data | BM Schilder | https://github.com/neurogenomics/scNLP | TRUE | TRUE | R | package | GitHub | ||
| scKirby | Automated ingestion and conversion of various single-cell data formats | BM Schilder | https://github.com/neurogenomics/scKirby | TRUE | TRUE | R, Python | package | GitHub | ||
| geneshotR | R package for querying and processing results from Geneshot. | BM Schilder | https://github.com/bschilder/geneshotR | FALSE | TRUE | R | package | GitHub | ||
| templateR | Self-updating template for developing R packages | BM Schilder | https://github.com/neurogenomics/templateR | https://doi.org/10.21203/rs.3.rs-2399015/v1 | TRUE | TRUE | R | package | GitHub | |
| echoverseTemplate | Self-updating template for creating echoverse R packages. | BM Schilder | https://github.com/RajLabMSSM/echoverseTemplate/ | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R | package | GitHub | |
| echolocatoR | R package for end-to-end statistical and functional fine-mapping with extensive dataset access | BM Schilder, J Humphrey, T Raj | https://github.com/RajLabMSSM/echolocatoR | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R, Python | package | GitHub | |
| echodata | Examples of fine-mapped GWAS summary statistics, data formatting functions, and API access to the echolocatoR Fine-mapping Portal | BM Schilder | https://github.com/RajLabMSSM/echodata | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R | package | GitHub | |
| echoannot | Functions for annotating genomic data with annotations and epigenomic data | BM Schilder | https://github.com/RajLabMSSM/echoannot | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R | package | GitHub | |
| echoplot | R package for LocusZoom-inspired GWAS/QTL visualization, with API access to LD panels | BM Schilder | https://github.com/RajLabMSSM/echoplot | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R | package | GitHub | |
| echoconda | Various utility functions to find, build, and use conda environments from within R | BM Schilder | https://github.com/RajLabMSSM/echoconda | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R, Python | package | GitHub | |
| echotabix | Tabix indexing and querying | BM Schilder | https://github.com/RajLabMSSM/echotabix | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R, Python | package | GitHub | |
| echoLD | LD downloading and processing. | BM Schilder | https://github.com/RajLabMSSM/echoLD | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R, Python | package | GitHub | |
| echofinemap | Statistical and functional fine-mapping functions. | BM Schilder | https://github.com/RajLabMSSM/echofinemap | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R, Python | package | GitHub | |
| echodeps | Creates interactive dependency networks for R packages | BM Schilder | https://github.com/RajLabMSSM/echodeps | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R | package | GitHub | |
| echogithub | Access and process metadata from GitHub | BM Schilder | https://github.com/RajLabMSSM/echogithub | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R | package | GitHub | |
| devoptera | Practical tools for R developers | BM Schilder | https://github.com/RajLabMSSM/devoptera | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R | package | GitHub | |
| downloadR | Single- and multi-threaded downloading functions | BM Schilder | https://github.com/RajLabMSSM/downloadR | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R | package | GitHub | |
| catalogueR | R package for rapid API-access and colocalization of summary statistics from eQTL Catalogue | BM Schilder | https://github.com/RajLabMSSM/catalogueR | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R | package | GitHub | |
| TopicModeler | Proprietary Python package to run advanced topic modeling on text corpuses. | BM Schilder | NA | NA | NA | TRUE | FALSE | Python | package | GitHub |
| LinkReporter | Proprietary Python package to extract job postings and company employee listings from LinkedIn and generate interactive business intelligence reports. | BM Schilder | NA | NA | NA | TRUE | FALSE | Python | package | GitHub |
| PubReporter | Proprietary Python package for extract relevant scientific literature, gather citations, and generate interactive business intelligence reports. | BM Schilder | NA | NA | NA | TRUE | FALSE | Python | package | GitHub |
| Rare Disease Celltyping Portal | Web portal connecting to multiple R Shiny apps to explore, visualize, and download cell type-specific enrichment results and systematically prioritised gene targets for over 6,000 rare disease phenotypes. | R Gordon-Smith, BM Schilder | https://github.com/neurogenomics/rare_disease_celltyping_apps | https://neurogenomics.github.io/rare_disease_celltyping_apps/home | https://doi.org/10.1101/2023.02.13.23285820 | TRUE | TRUE | R | database | shinyapps.io |
| Parkinson’s Disease Omics Review | Data and code associated with the Parkinson’s Disease review paper by Schilder, Navarro & Raj (Neurobiology of Disease, 2021) | BM Schilder, E Navarro, T Raj | https://github.com/RajLabMSSM/PD_omics_review | https://rajlabmssm.github.io/PD_omics_review/ | https://doi.org/10.1016/j.nbd.2021.105580 | TRUE | TRUE | R | database | GitHub |
| Selective Vulnerability Meta-analysis | Selective Vulnerability Meta-analysis: Shiny app dedicated to the exploration and dissemination of meta-analysed cell counts manually curated and harmonised from the Parkinson’s Disease literature | https://github.com/neurogenomics/SelectiveVulnerabilityMetaAnalysis | TRUE | TRUE | R | database | shinyapps.io | |||
| MAGMA Files Public | Gene enrichment files for hundreds of GWAS generated with Multi-marker Analysis of GenoMic Annotation (MAGMA) for use in downstream analyses | https://github.com/neurogenomics/MAGMA_Files_Public | TRUE | TRUE | R | database | GitHub | |||
| echolocatoR Fine-mapping Portal | Access to interactive plots and fine-mapping results across many GWAS/QTL datasets using echolocatoR | https://github.com/RajLabMSSM/Fine_Mapping_Shiny | https://rajlab.shinyapps.io/Fine_Mapping_Shiny | https://doi.org/10.1093/bioinformatics/btab658 | TRUE | TRUE | R | database | shinyapps.io | |
| COVID-19 Patient Tracker | Web app for summarizing and visualizing real-time EHR data of COVID-19 patients within the Mount Sinai Health System | BM Schilder | TRUE | FALSE | Python | web app | GitHub | |||
| Tensor Decomposition Shiny App | Interactive application to explore and download all results and plots from Ramdhani et al. (PLOS Genetics, 2020) | S Ramdhani, E Navarro, E Udine, AG Efthymiou, BM Schilder, M Parks, A Goate, T Raj | https://github.com/RajLabMSSM/Tensor_myeloid | https://rajlab.shinyapps.io/Tensor_myeloid | https://doi.org/10.1101/499509 | TRUE | TRUE | R | database | shinyapps.io |
| Hippocampal Evolution | Interactive code, results and visualization for the manuscript “Evolutionary selective pressures dramatically expanded and reorganized the human hippocampal complex” | BM Schilder | https://github.com/bschilder/Hippo_Eco | https://bschilder.github.io/Hippo_Eco/HPsubfield_eco | https://doi.org/10.1002/cne.24822 | TRUE | TRUE | R | web app | GitHub |
| Geneshot | Flexible tool to identify genes associated with any biomedical term and to predict novel target genes | A Lachmann, BM Schilder, ML Wojciechowicz, D Torre, MV Kuleshov, AB Keenan, A Ma’ayan | https://amp.pharm.mssm.edu/geneshot | https://doi.org/10.1093/nar/gkz393 | TRUE | FALSE | Java, Python, JavaScript, HTML, CSS | web app | maayanlab.cloud | |
| X2K | eXpression 2 Kinases (X2K) Web: Automated computational pipeline to infer kinase regulators from weighted or unweighted gene lists | DJB Clarke, MV Kuleshov, BM Schilder, D Torre, ME Duffy, AB Keenan, A Lachmann, AS Feldmann, GW Gundersen, MC Silverstein, Z Wang | https://amp.pharm.mssm.edu/X2K | https://doi.org/10.1093/nar/gky458 | TRUE | FALSE | Java, Python, JavaScript, HTML, CSS | web app | maayanlab.cloud | |
| Personal Website | BM Schilder, M Parker | https://github.com/bschilder/BMSchilder | https://bschilder.github.io/BMSchilder | TRUE | TRUE | HTML, CSS, JavaScript | website | GitHub | ||
| Official Raj Lab Website | BM Schilder | https://github.com/RajLabMSSM/RajLab_website | https://www.rajlab.org | TRUE | TRUE | HTML, CSS, JavaScript | website | GitHub |