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@RajLabMSSM

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bschilder/README.md

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Summary

Full Report

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Projects

A list of software, databases, websites, and other projects that I’ve created or made significant contributions to.

R Packages

All Projects

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 http://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 http://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 http://www.rajlab.org TRUE TRUE HTML, CSS, JavaScript website GitHub

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