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MIRA (Multimodal models for Integrated Regulatory Analysis) for joint single-cell RNA-seq and ATAC-seq analysis. Provides probabilistic topic modeling, joint representation learning, pseudotime trajec
Use with AI
Install the MCP server or CLI to instantly fetch MIRA --- Multimodal Models for Integrated Regulatory Analysis documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/mira
HTSeq — Python framework for high-throughput sequencing data analysis, primarily used for counting aligned reads overlapping genomic features (genes, exons) from SAM/BAM/CRAM files using GTF/GFF annot
2 shared topics • 2 shared operations
salmon — Fast, bias-aware transcript quantification from RNA-seq data using selective alignment to the transcriptome. Supports bulk RNA-seq (mapping-based and alignment-based modes), single-cell RNA-s
2 shared topics • 2 shared operations
Salmon is an ultrafast, bias-correcting tool for quantifying transcript abundances from RNA-seq reads using quasi-mapping or selective alignment. Alevin is Salmon's single-cell mode for generating cel
2 shared topics • 2 shared operations
Scanorama -- efficient batch correction and integration of heterogeneous single-cell RNA-seq datasets using panoramic stitching. Aligns and merges multiple scRNA-seq experiments via mutual nearest nei
2 shared topics • 2 shared operations
sciPENN — neural network model for single-cell protein expression imputation and multi-omics integration. Transfers protein predictions from CITE-seq (paired RNA+protein) training data to unpaired RNA
2 shared topics • 2 shared operations