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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
In the realm of cancer research, grasping the intricacies of intratumor heterogeneity and its interplay with the immune system is paramount for deciphering treatment resistance and tumor progression. While single-cell RNA sequencing unveils diverse transcriptional programs, the challenge persists in automatically discerning malignant cells from non-malignant ones within complex datasets featuring varying coverage depths. Thus, there arises a compelling need for an automated solution to this classification conundrum. SCEVAN (De Falco et al., 2023), a variational algorithm, is designed to autonomously identify the clonal copy number substructure of tumors using single-cell data. It automatically separates malignant cells from non-malignant ones, and subsequently, groups of malignant cells are examined through an optimization-driven joint segmentation process.
BioTuring
Single-cell RNA-seq datasets in diverse biological and clinical conditions provide great opportunities for the full transcriptional characterization of cell types. However, the integration of these datasets is challeging as they remain biological and techinical differences. **Harmony** is an algorithm allowing fast, sensitive and accurate single-cell data integration.
T-cells
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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.