{"id":120,"date":"2020-06-09T13:54:07","date_gmt":"2020-06-09T18:54:07","guid":{"rendered":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/?page_id=120"},"modified":"2024-03-13T12:20:15","modified_gmt":"2024-03-13T17:20:15","slug":"software","status":"publish","type":"page","link":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/software\/","title":{"rendered":"Software"},"content":{"rendered":"<p>This page contains the tools and software packages we have developed @ Maize Zhou Lab or previously @ Stanford.<\/p>\n<p>Please visit our <a href=\"https:\/\/github.com\/maiziezhoulab\">Lab GitHub page<\/a>\u00a0for the latest releases.<\/p>\n<ul>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/BenchmarkST\"><span style=\"color: #000000\">BenchmarkST: Benchmarking clustering, alignment, and integration methods for spatial transcriptomics.\u00a0<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/CNVeil\"><span style=\"color: #000000\">CNVeil: accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/VolcanoSV\"><span style=\"color: #000000\">VolcanoSV: accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/MaskGraphene\/\"><span style=\"color: #000000\">MaskGraphene: advancing joint embedding, clustering, and batch correction for spatial transcriptomics using graph-based self-supervised learning.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/RegionIndel\"><span style=\"color: #000000\">RegionIndel: Large indel detection in region-based phased diploid assemblies from linked-reads.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/ADEPT\"><span style=\"color: #000000\">ADEPT: autoencoder with differentially expressed genes and imputation for a robust spatial transcriptomics clustering.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/LRSV_combo\"><span style=\"color: #000000\">LRSV_combo: long read based SV calling tools analysis.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/embSV\"><span style=\"color: #000000\">embSV: haplotype-phasing of long-read HiFi data to enhance structural variant detection through a Skip-Gram model.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/AquilaDeepFilter\"><span style=\"color: #000000\">AquilaDeepFilter: automated filtering of genome-wide large deletions through an ensemble deep learning framework.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/Bfimpute\"><span style=\"color: #000000\">Bfimpute: a Bayesian factorization method to recover single-cell RNA sequencing data.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/RNN_workingmemoryaccuracy\"><span style=\"color: #000000\">RNN_workingmemoryaccuracy: neural mechanisms of working memory accuracy revealed by recurrent neural networks.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/RNN_BrainMaturation\"><span style=\"color: #000000\">RNN_BrainMaturation: emergence of prefrontal neuron maturation properties by training recurrent neural networks in cognitive tasks.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziezhoulab\/Autism_genepheno\"><span style=\"color: #000000\">Autism_genepheno: text mining of gene-phenotype associations reveals new phenotypic profiles of autism-associated genes.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziex\/MARS\"><span style=\"color: #000000\">MARS: a package for multiple samples alignment-base structural variant calling and refinement.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziex\/Aquila_stLFR\"><span style=\"color: #000000\">Aquila_stLFR: diploid genome assembly based structural variant calling package for stLFR linked-read.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziex\/Aquila\"><span style=\"color: #000000\">Aquila: diploid personal genome assembly and comprehensive variant detection based on linked-reads.<\/span><\/a><\/li>\n<li><a href=\"https:\/\/github.com\/maiziex\/HAPDeNovo\"><span style=\"color: #000000\">HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data.<\/span><\/a><\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>This page contains the tools and software packages we have developed @ Maize Zhou Lab or previously @ Stanford. Please visit our Lab GitHub page\u00a0for the latest releases. BenchmarkST: Benchmarking clustering, alignment, and integration methods for spatial transcriptomics.\u00a0 CNVeil: accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data. VolcanoSV:&#8230;<\/p>\n","protected":false},"author":242,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"tags":[],"class_list":["post-120","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/pages\/120","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/users\/242"}],"replies":[{"embeddable":true,"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/comments?post=120"}],"version-history":[{"count":44,"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/pages\/120\/revisions"}],"predecessor-version":[{"id":1449,"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/pages\/120\/revisions\/1449"}],"wp:attachment":[{"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/media?parent=120"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/tags?post=120"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}