Pinned Repositories
ascend
Analysis of Single Cell Expression, Normalization and Differential expression
BBMap
(Not Offical) BBMap short read aligner, and other bioinformatic tools.
BrainDeconBenchmark
This study benchamrked the performance of existing cell deconvolution methods with human brain transcriptome and evaluated the biological applications of deconvoluted data in eQTL mapping and differential expression analysis.
BrCa_cell_atlas
Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
cellhint
A tool for semi-automatic cell type harmonization and integration
CortexCellDeconv
deconv_benchmark
deconv_matching_bulk_scnRNA
Repository for "Effective methods for bulk RNA-seq deconvolution using scRNA-seq and snRNA-seq derived transcriptomes"
DecOT
Zipper_plot
Zipper plot: visualizing transcriptional activity of genomic regions
favilaco's Repositories
favilaco/deconv_benchmark
favilaco/deconv_matching_bulk_scnRNA
Repository for "Effective methods for bulk RNA-seq deconvolution using scRNA-seq and snRNA-seq derived transcriptomes"
favilaco/Zipper_plot
Zipper plot: visualizing transcriptional activity of genomic regions
favilaco/ascend
Analysis of Single Cell Expression, Normalization and Differential expression
favilaco/BBMap
(Not Offical) BBMap short read aligner, and other bioinformatic tools.
favilaco/BrainDeconBenchmark
This study benchamrked the performance of existing cell deconvolution methods with human brain transcriptome and evaluated the biological applications of deconvoluted data in eQTL mapping and differential expression analysis.
favilaco/BrCa_cell_atlas
Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".
favilaco/cellhint
A tool for semi-automatic cell type harmonization and integration
favilaco/CortexCellDeconv
favilaco/DecOT
favilaco/DWLS
Gene expression deconvolution using dampened weighted least squares
favilaco/Libra
favilaco/paste_reproducibility
favilaco/gsdensity
favilaco/GSDensity_manuscript_code
favilaco/neuroblastoma_gene_signature
Validate a gene signature for evaluating the survival of patients with neuroblastoma.
favilaco/PICALO
eQTL interaction optimization using expectation maximization
favilaco/RADs
favilaco/recount3_networks
Scripts required to replicate the analysis in - "Aggregation of publicly available RNA-seq experiments improves inference of consensus and tissue-specific Gene Co-expression Networks"
favilaco/recover-counts
Recover transcript counts from log-normalized UMI counts data.
favilaco/rosmap_mediation_paper
favilaco/sc-SHC
Significance analysis for clustering single-cell RNA-sequencing data
favilaco/sc-type
favilaco/SEACells
SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data
favilaco/spatial_scog_workshop_2022
Tutorials for the SCOG Virtual Workshop ‘Spatial transcriptomics data analysis in Python’ - May 23-24, 2022
favilaco/spatialHallmarks_paper
favilaco/Strategies-for-cellular-deconvolution-in-human-brain-RNA-sequencing-data
favilaco/vsn-pipelines
A repository of pipelines for single-cell data in Nextflow DSL2