국내 유일의 클라우드 기반 통합 데이터 분석 서비스
공개된 프로그램 및 파이프라인 열람을 통한 분석 기초 정보 확인분석 프로그램
Bio-Express에는 총 41개의 프로그램이 등록되어 있습니다.
HaplotypeCallerSpark
This is an implementation of HaplotypeCaller using spark to distribute the computation. It is still in an early stage of development and does not yet support all the options that the non-spark version does. Specifically it does not support the --dbsnp, --comp, and --bam-output options.
- IDBX03-20221219-0474
- 대분류Bioinformatics
- 중분류Whole-Genome-Sequencing
- 구동환경BX_ENV_01
- 언어Bash
- 코어수Multi
- 버전4.2.0.0
- 등록자bioex
- 등록일2022-12-19
- 수정일2022-12-23
#gatk
fastp
Description : Atool designed to provide fast all-in-one preprocessing for FastQ files
- IDBX03-20221123-0465
- 대분류Tools
- 중분류Annovar
- 구동환경BX_ENV_00
- 언어Bash
- 코어수Single
- 버전0.20.1
- 등록자tester
- 등록일2022-12-14
- 수정일2022-12-14
#fastp
FastQC
FastQC is a program designed to spot potential problems in high througput sequencing datasets. It runs a set of analyses on one or more raw sequence files in fastq or bam format and produces a report which summarises the results.
- IDBX03-20220112-0270
- 대분류Bioinformatics
- 중분류Whole-Genome-Sequencing
- 구동환경BX_ENV_00
- 언어Bash
- 코어수Single
- 버전0.11.9
- 등록자bioex
- 등록일2022-01-12
- 수정일2022-01-12
#FastQC
gene_expr_visualization
Gene expression visualization
- IDBX03-20211203-0263
- 대분류Bioinformatics
- 중분류SPATIAL_scRNA_seq
- 구동환경NA
- 언어Python
- 코어수Multi
- 버전1.0
- 등록자cogate
- 등록일2021-12-03
- 수정일2021-12-08
#gene_expr_visualization
Find_cluster_marker
Finding differentially expressed features (cluster biomarkers)
- IDBX03-20211201-0261
- 대분류Bioinformatics
- 중분류SPATIAL_scRNA_seq
- 구동환경NA
- 언어Python
- 코어수Multi
- 버전1.0
- 등록자cogate
- 등록일2021-12-01
- 수정일2021-12-07
#cluster marker
Integration_scRNA_data
integration scRNA-seq data with spatial scRNA-seq data
- IDBX03-20211201-0259
- 대분류Bioinformatics
- 중분류SPATIAL_scRNA_seq
- 구동환경NA
- 언어Python
- 코어수Multi
- 버전1.0
- 등록자cogate
- 등록일2021-12-01
- 수정일2021-12-08
#integration with signle-cell data
Clustering
Seurat spatial scRNA analysis pipeline : Dimensionality reduction, clustering, and visualization
This module process : 1) RunPCA, 2) FindNeighbors, 3) FindClusters, 4) RunUMAP
- IDBX03-20211130-0255
- 대분류Bioinformatics
- 중분류SPATIAL_scRNA_seq
- 구동환경NA
- 언어Python
- 코어수Single
- 버전1.0
- 등록자cogate
- 등록일2021-11-30
- 수정일2021-12-08
#spatial_scRNA_clustering
Preprocessing
Seurat spatial scRNA-seq data preprocessing
- IDBX03-20211129-0253
- 대분류Bioinformatics
- 중분류SPATIAL_scRNA_seq
- 구동환경NA
- 언어Python
- 코어수Single
- 버전1.0
- 등록자cogate
- 등록일2021-11-29
- 수정일2021-12-31
#Seurat##Spatial_scRNA-seq
Spaceranger
Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA.
Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images.
- IDBX03-20211123-0251
- 대분류Bioinformatics
- 중분류SPATIAL_scRNA_seq
- 구동환경NA
- 언어Python
- 코어수Multi
- 버전1.0
- 등록자cogate
- 등록일2021-11-23
- 수정일2021-12-08
#Visium Spatial gene Expression##mapping
Slice_highly_variable_genes
Delete everything except highly variable genes.
Necessaray for computing efficiency.
- IDBX03-20211118-0243
- 대분류Bioinformatics
- 중분류Single-Cell-RNA-Sequencing
- 구동환경BX_ENV_00
- 언어Python
- 코어수Single
- 버전0.1
- 등록자bioex
- 등록일2021-11-18
- 수정일2021-11-18
#slice#cutoff