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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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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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r-dplyr
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public |
A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
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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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cellphonedb
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public |
CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
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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 |
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python-circos
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public |
Circos is one of the most popular software for visualizing genomic similarities and features. However, its execution process is complicated and requires multiple original config files for the visualizations. Additionally, Circos is written in Perl, which limits its integration with other software for biological analysis. On the other hand, Python has been applied for various biological software packages. Therefore, by combining these packages, researchers can complete most of the required analysis. Nevertheless, Python lacks a library for drawing Circos plots, even though Circos software has been developed for more than a decade. Here, we provide a python Matplotlib based circular genome visualization package pyCiros. Users easily and quickly visualize genomic features and comparative genome analysis results by specifying annotated sequence files such as GenBank files.
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2025-03-25 |
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biocolabsdk
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public |
A set of python modules for accessing BioTuring Ecosystem on BioColab private server
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2025-03-25 |
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bioturing-connector
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public |
A set of python modules for accessing BBrowserX on private server
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2025-03-25 |
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bioflex
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public |
A set of python modules for accessing BioTuring single-cell database
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2025-03-25 |
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r-scenic
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public |
SCENIC workflow
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2025-03-25 |
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r-music
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public |
Companion package to: A bulk tissue deconvolution method with multi-subject single cell expression reference. This package provide functions to estimate bulk tissue cell type proportions with multi-subject single cell expression as reference.
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2025-03-25 |
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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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r-signac
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public |
A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
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2025-03-25 |
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r-vctrs
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public |
Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.
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2025-03-25 |
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r-nichenetr
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public |
This package allows you the investigate intercellular communication from a computational perspective. More specifically, it allows to investigate how interacting cells influence each other's gene expression. Functionalities of this package (e.g. including predicting extracellular upstream regulators and their affected target genes) build upon a probabilistic model of ligand-target links that was inferred by data-integration.
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2025-03-25 |
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r-emoa
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public |
Collection of building blocks for the design and analysis of evolutionary multiobjective optimization algorithms.
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2025-03-25 |
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r-ibridge
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public |
The development of immune checkpoint-based therapies has been a major advancement in the treatment of cancer with a subset of patients exhibiting dramatic and durable responses across a variety of tumor types. A predictive biomarker for the immunotherapy response is the pre-existing T cell infiltration in the tumor immune microenvironment (TIME). Bulk transcriptomics-based approaches can crudely and indirectly quantify the level of T-cell infiltration using metagenes/deconvolution methods, and therefore can differentiate inflamed and immunologically cold tumors. However, these bulk techniques are unable to identify biomarkers of individual cell types in the TIME. More recently, single-cell RNA sequencing (scRNAseq) based assays have been used to profile a granular account of the TIME. To our knowledge there is no method of identifying patients with T-cell inflamed TIME using both scRNAseq and bulk transcriptomics data. Here, we demonstrate a method, called Identifying Biological Relationships In Dark matter of Genomics Entities (I-BRIDGE), which integrates TCGA bulk RNA-seq data with the malignant/epithelial portion of scRNAseq data to identify patients with T-cell inflamed TIME. Using this method, we report the markers of inflamed phenotypes in malignant cells, myeloid cells and fibroblasts. Thus, we identify Type I and Type II interferon pathways as dominant signals, especially in malignant and myeloid cells. This contrasts with the immune cell metagenes as the main markers of inflamed cancers identified in bulk datasets. These cell-type specific markers potentially include causative targetable genes that can transform a cold TIME to an inflamed one when modulated. In addition, I-BRIDGE can be applied to in vitro grown cancer cell lines and can identify the cell lines that are likely to be adapted from inflamed/cold patient tumors.
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2025-03-25 |
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r-card
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public |
CARD is a reference-based deconvolution method that estimates cell type composition in spatial transcriptomics based on cell type specific expression information obtained from a reference scRNA-seq data. A key feature of CARD is its ability to accommodate spatial correlation in the cell type composition across tissue locations, enabling accurate and spatially informed cell type deconvolution as well as refined spatial map construction. CARD relies on an efficient optimization algorithm for constrained maximum likelihood estimation and is scalable to spatial transcriptomics with tens of thousands of spatial locations and tens of thousands of genes. CARD is implemented as an open-source R package, freely available at www.xzlab.org/software.html
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2025-03-25 |
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r-wrmisc
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public |
The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc. Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. Many times large experimental datasets need some additional filtering, adequate functions are provided. Batch reading (or writing) of sets of files and combining data to arrays is supported, too. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
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2025-03-25 |
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r-seuratwrappers
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public |
SeuratWrappers is a collection of community-provided methods and extensions for Seurat, curated by the Satija Lab at NYGC. These methods comprise functionality not presently found in Seurat, and are able to be updated much more frequently.
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2025-03-25 |
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r-celltrek
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public |
CellTrek is a computational toolkit that can directly map single cells back to their spatial coordinates in tissue sections based on scRNA-seq and ST data. The CellTrek toolkit also provides two downstream analysis modules, including SColoc for spatial colocalization analysis and SCoexp for spatial co-expression analysis.
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2025-03-25 |
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r-cellchat
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public |
an open source R tool that infers, visualizes and analyzes the cell-cell communication networks from scRNA-seq data.
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2025-03-25 |
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r-packcircles
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public |
Algorithms to find arrangements of non-overlapping circles.
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2025-03-25 |
