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Description
Python is a widely used high-level, general-purpose, interpreted, dynamic programming language. Its design philosophy emphasizes code readability, and its syntax allows programmers to express concepts in fewer lines of code than would be possible in languages such as C++ or Java. The language provides constructs intended to enable clear programs on both a small and large scale. We provide some meta packages for convenience. To get a CPython flavour, use conda install cpython To get the freethreading build (i.e. without the Global Interpreter Lock - GIL) conda install python-freethreading To get the default build (i.e. with the GIL) conda install python-gil To enable the use of the experimental JIT compiler in CPython conda install python-jit or set the environment variable PYTHON_JIT=1. Note that the JIT support is available for x86_64 builds only.
Utilized in BioStudio
1000
Platform:
linux-64
noarch
Related notebook
BioTuring
The development of large-scale single-cell atlases has allowed describing cell states in a more detailed manner. Meanwhile, current deep leanring methods enable rapid analysis of newly generated query datasets by mapping them into reference atlases. expiMap (‘explainable programmable mapper’) Lotfollahi, Mohammad, et al. is one of the methods proposed for single-cell reference mapping. Furthermore, it incorporates prior knowledge from gene sets databases or users to analyze query data in the context of known gene programs (GPs).
BioTuring
Single-cell RNA sequencing (scRNA-seq) data often encountered technical artifacts called "doublets" which are two cells that are sequenced under the same cellular barcode. Doublets formed from different cell types or states are called heterotypic and homotypic otherwise. These factors constrain cell throughput and may result in misleading biological interpretations. DoubletFinder (McGinnis, Murrow, and Gartner 2019) is one of the methods proposed for doublet detection. In this notebook, we will illustrate an example workflow of DoubletFinder. We use a 10x Genomics dataset which captures peripheral blood mononuclear cells (PBMCs) from a healthy donor stained with a panel of 31 TotalSeq™-B antibodies (BioLegend).
BioTuring
InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes. This is done by exploring expression intensity of genes across positions of tumor genome in comparison to a set of reference 'normal' cells. A heatmap is generated illustrating the relative expression intensities across each chromosome, and it often becomes readily apparent as to which regions of the tumor genome are over-abundant or less-abundant as compared to that of normal cells. **Infercnvpy** 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.