NGDC BIT

Category

Visualization

Bar Box Comutation Dot Forest Heatmap Histogram Lollipop Mafsummary Maftitv Manhattan Oncoprint PM-Adiversity PM-comp-cor PM-comp-func PM-comp-taxa PM-Distribution PM-Hcluster PM-Heatmap PM-Marker-Corr PM-Marker-RFscore PM-Marker-Test PM-Network PM-Pca PM-Pcoa PM-plot-taxa PM-rare-curv Q-Q Survival Upset Venn

Sequence alignment

BLAST Dotmatcher Dotpath Dottup Needle PM-Bdiversity PM-extract-rna PM-parallel-meta PM-pipeline PM-profiler Polydot Water

RNA Expression

Bulk RNA-seq Data Analysis Cancer Alternative Splicing Analysis CCLHunter CIRI-deep CIRI3 Cross-disease analysis Disease prediction Editing site annotation Editing site identification EFDetector FunGen Gene-disease network construction HELIX NCSelPred RNA-seq Analysis Single-cell RNA-seq Data Analysis SPIRAL TIVar diff TIVar predict Visualization of scRNA-seq Data Analysis Results

Variome analysis

BarcodeBLAST BarcodeFinder easyGWAS ExpPattern GeneFinder Haplotype analysis HapMap HapSnap LeadSNPFinder Pangolin LOCATOR Rice Varieties Identification Rice Yield Estimation SeqFetch VersionMap Wheat Head Estimation

Epigenome analysis

Age Predictor BS-RNA Comparative analysis in nucleosomes DMR Annotation DMR Toolkit Enrichment & Annotation Enrichment analysis in nucleosome occupancy EWAS Network Visualization GMQN IDMP Lollipop Plotter MRAS

Long non-coding RNA

Classification Functional Prediction ID conversion LGC lncbook-BLAST LncBot

Virus

COVID-19 genome variation annotation COVID-19 haplotype analysis Denovo Assembly Evolutionary tree Fastq-to-Variants Genealogy and Evolutionary Analysis Genome Annotation Genome Tracing InfluProto McAN Monkeypox virus genome variation annotation Monkeypox virus genome variation identification Pangolin COVID-19 Lineage Assigner SeqQC VENAS VISTA

Single-cell omics

Cell Type Comparator Cell Type Predictor FGOT GOT RegChat SCSES SpaDC SpaMI TACOS

Image Processing

Image Cropping Image Denoising Image Flipping Image Partitioning Image Resizing

Others

Composition analysis Cross-model analysis Cross-species analysis Cross-stages analysis Homolog Finder LUTLSRS MEFE MIA Microbiome Search Engine MT-tracker ncRNA-eQTL PM-parse-mip PM-predict-func PM-predict-func-contribute PM-predict-func-nsti PM-rand-rare PM-select-func PM-select-taxa PM-split-seq TaxaCal

User Manual

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Data

Path to the normalized RNA data file

Input data text

Upload a file

Path to the normalized ATAC data file

Input data text

Upload a file

Path to the RNA cluster info file

Input data text

Upload a file

Path to the containing peak-gene_mt file

Input data text

Upload a file

Path to the corr matrix file (snn or wnn matrix)

Input data text

Upload a file

Parameters

Input type (e.g., paired or unpaired)

Whether to use minibatch (default 0 for not use)

Batch size for mini-batch computing (optional, required if minibatch = 1)

Epsilon for tensor computation

Parameter rho_mu

Parameter rho_nu

Maximum number of iterations

Stopping threshold

Lambda for regularization

alignment mode (default "ATAC2RNA", else "RNA2ATAC")

ATAC2RNA

RNA2ATAC

References

Instructions

FGOT is an interpretable integration tool for single-cell and spatial multi-omics data.

Contributor(s)

Chenghui Yang

2022282110116@whu.edu.cn

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