Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
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Updated
Sep 28, 2024 - Python
Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images (https://oncopathtk.org)
Calibrated clustering with artificial variables to avoid over-clustering in single-cell RNA-sequencing
Single-cell dimensionality reduction evaluation and benchmarking toolkit
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
The study of how cancer cells gain stemness.
Single-cell dimensionality reduction toolkit
Python code for cross-condition label refinement in single-cell data with HiDDEN
Swift Phenotypic Analysis of Cells
Haplotype-aware CNV analysis from single-cell RNA-seq
Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function
Transcriptomic profiling of transcription factor induced human PSC-derived retinal ganglion cells
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
TRIAGE is provided here as an R package comprised of three tools: 1) TRIAGEgene, 2) TRIAGEcluster, and 3) TRIAGEparser, along with a set of functions that streamlines creation of publication-ready figures and facilitates smoother data analysis.
A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like pipeline toolkit for the R language.
The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
scripts for scRNA-Seq/scATAC-Seq
QuantQC is a package for quality control (QC) of single-cell proteomics data. It is optimized to work with nPOP, a method for massively parallel sample preparation on glass slides.
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