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r-monocle3
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public |
Monocle 3 performs clustering, differential expression and trajectory analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle 3 also performs differential expression analysis, clustering, visualization, and other useful tasks on single-cell expression data. It is designed to work with RNA-Seq data, but could be used with other types as well.
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2025-03-25 |
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pyflowsom
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public |
A Python implementation of the SOM training functionality of FlowSOM
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2025-03-25 |
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alpineer
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public |
Toolbox for Multiplexed Imaging. Contains scripts and little tools which are used throughout ark-analysis, mibi-bin-tools, and toffy.
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2025-03-25 |
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moods-python
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public |
MOODS: Motif Occurrence Detection Suite
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2025-03-25 |
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ucsc_genomes_downloader
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public |
Python package to quickly download genomes from the UCSC.
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2025-03-25 |
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cellrank
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public |
CellRank: dynamics from multi-view single-cell data
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2025-03-25 |
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r-scevan
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public |
R package that starting from the raw count matrix of scRNA data automatically classifies the cells present in the biopsy by segregating non-malignant cells of tumor microenviroment from the malignant cells and also characterizes the clonal structure of these malignant cells.
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2025-03-25 |
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r-yagst
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public |
This is a collection of wrappers to the Wilcoxon test to run competitive gene set tests and comparison between imbalanced datasets.
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2025-03-25 |
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scarches
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public |
Transfer learning with Architecture Surgery on Single-cell data
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2025-03-25 |
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schpl
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public |
Hierarchical progressive learning pipeline for single-cell RNA-sequencing datasets
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2025-03-25 |
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infercnvpy
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public |
Infercnv is a scalable python library to infer copy number variation (CNV) events from single cell transcriptomics data. It is heavliy inspired by InferCNV, but plays nicely with scanpy and is much more scalable.
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2025-03-25 |
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gtfparse
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public |
GTF Parsing
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2025-03-25 |
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pertpy
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public |
Perturbation Analysis in the scverse ecosystem.
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2025-03-25 |
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sparsecca
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public |
A full implementation of sparse CCA.
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2025-03-25 |
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switchlang
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public |
Adds switch blocks to the Python language.
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2025-03-25 |
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flit-core
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public |
Distribution-building parts of Flit. See flit package for more information
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2025-03-25 |
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r-doubletfinder
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public |
DoubletFinder identifies doublets by generating artificial doublets from existing scRNA-seq data and defining which real cells preferentially co-localize with artificial doublets in gene expression space. Other DoubletFinder package functions are used for fitting DoubletFinder to different scRNA-seq datasets. For example, ideal DoubletFinder performance in real-world contexts requires (I) Optimal pK selection and (2) Homotypic doublet proportion estimation. pK selection is achieved using pN-pK parameter sweeps and maxima identification in mean-variance-normalized bimodality coefficient distributions. Homotypic doublet proportion estimation is achieved by finding the sum of squared cell annotation frequencies. For more information, see our Cell Sysmtes paper https://www.cell.com/cell-systems/fulltext/S2405-4712(19)30073-0 and our github https://github.com/chris-mcginnis-ucsf/DoubletFinder
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2025-03-25 |
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giotto
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public |
Web development simplified. An MVC framework supporting Python 3.
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2025-03-25 |
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py-bcrypt
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public |
bcrypt password hashing and key derivation
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2025-03-25 |
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irc
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public |
IRC (Internet Relay Chat) protocol library for Python
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2025-03-25 |
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ctxcore
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public |
the blessed package to manage your versions by scm tags
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2025-03-25 |
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pyscenic
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public |
Python implementation of the SCENIC pipeline for transcription factor inference from single-cell transcriptomics experiments.
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2025-03-25 |
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multiprocessing_on_dill
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public |
A friendly fork of multiprocessing which uses dill instead of pickle
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2025-03-25 |
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cellphonedb
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public |
No Summary
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2025-03-25 |
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ktplotspy
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public |
Python library for plotting Cellphonedb results. Ported from ktplots R package.
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2025-03-25 |
