crr-labels 1.1.1

FANTOM

要检索FANTOM启动子和增强子，您可以按照以下步骤操作

from crr_labels import fantom

enhancers, promoters = fantom(
    cell_lines=["HelaS3", "GM12878"], # list of cell lines to be considered.
    window_size=200, # window size to use for the various regions.
    genome = "hg19", # considered genome version. Currently supported only "hg19".
    center_enhancers = "peak", # how to center the enhancer window, either around "peak" or the "center" of the region.
    enhancers_threshold = 0, # activation threshold for the enhancers.
    promoters_threshold = 5, # activation threshold for the promoters.
    drop_always_inactive_rows = True, # whether to drop the rows where no activation is detected for every row.
    binarize = True, # whether to return the data binary-encoded, zero for inactive, one for active.
    nrows = None # the number of rows to read, useful when testing pipelines for creating smaller datasets.
)

该库将下载并解析fantom项目原始数据，并为所需细胞系返回两个DataFrame。请考虑阅读方法的docstring以获取有关方法的更深入信息。

主要步骤如下

• 从fantom_data.json文件中指定的链接检索fantom数据集的原始文件

• 增强子和启动子的窗口将扩展或压缩到给定的窗口大小。特别是

  • 增强子的窗口可以是“center”模式，以区域中心为中心，或者“peak”模式，以峰值为中心。

  • 启动子的窗口在正链上从启动子末尾上游，在负链上从启动子开始下游。

• 对于某个细胞系存在多个实验时，例如对于“HelaS3”，执行激活峰值的平均值。

• 可选（默认情况下）删除始终不活跃的行。您可以使用参数“drop_always_inactive_rows”指定此行为。

Roadmap

要检索路线图促进剂和增强子，您可以按照以下步骤操作

from crr_labels import roadmap

enhancers, promoters = roadmap(
    cell_lines = ["HelaS3", "GM12878"], # List of cell lines to be considered.
    window_size = 200, # Window size to use for the various regions.
    genome = "hg19", # Considered genome version. Currently supported only "hg19".
    states = 18, # Number of the states of the model to consider. Currently supported only "15" and "18".
    enhancers_labels = ("7_Enh", "9_EnhA1", "10_EnhA2"), # Labels to encode as active enhancers.
    promoters_labels = ("1_TssA",), # Labels to enode as active promoters.
    nrows = None # the number of rows to read, useful when testing pipelines for creating smaller datasets.
)

建议阅读方法文档字符串以获取有关该方法的更深入信息。

FANTOM

以下数据集包含了GM12878、HelaS3、HepG2、K562、A549、H1、H9、JURKAT、MCF7、HEK293、Caco2、HL60和PC3细胞系的实验数据。

待办事项：渲染数据集

Roadmap

以下数据集包含了GM12878、HelaS3、HepG2、K562、A549、H1、H9、DND41、HUES48、HUES6、HUES64和IMR90细胞系的实验数据。

待办事项：一旦我们确定要使用的新状态，将立即添加更新的处理标签。