Home Page
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
Classification of tumor and normal cells in the tumor microenvironment from scRNA-seq data is an ongoing challenge in human cancer study. Copy number karyotyping of aneuploid tumors (***copyKAT***) (Gao, Ruli, et al., 2021) is a method proposed for identifying copy number variations in single-cell transcriptomics data. It is used to predict aneuploid tumor cells and delineate the clonal substructure of different subpopulations that coexist within the tumor mass. In this notebook, we will illustrate a basic workflow of CopyKAT based on the tutorial provided on CopyKAT's repository. We will use a dataset of triple negative cancer tumors sequenced by 10X Chromium 3'-scRNAseq (GSM4476486) as an example. The dataset contains 20,990 features across 1,097 cells. We have modified the notebook to demonstrate how the tool works on BioTuring's platform.
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
Geneformer is a foundation transformer model pretrained on a large-scale corpus of ~30 million single cell transcriptomes to enable context-aware predictions in settings with limited data in network biology. Here, we will demonstrate a basic workflow to work with ***Geneformer*** models. These notebooks include the instruction to: 1. Prepare input datasets 2. Finetune Geneformer model to perform specific task 3. Using finetuning models for cell classification and gene classification application