معرفی شرکت ها

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

تبلیغات ما

مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.

مشاهده بیشتر

توضیحات

DiffDomain can test the significant difference of TADs on chromatin.

ویژگی	مقدار
سیستم عامل	-
نام فایل	diffDomain-py3-0.1.9
نام	diffDomain-py3
نسخه کتابخانه	0.1.9
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	Dechao Tian
ایمیل نویسنده	tiandch@mail.sysu.edu.cn
آدرس صفحه اصلی	https://github.com/Tian-Dechao/diffDomain
آدرس اینترنتی	https://pypi.org/project/diffDomain-py3/
مجوز	-

diffDomain ========== A short description ------------------- diffDomain is a new computational method for identifying reorganized TADs using chromatin contact maps from two biological conditions. A long description diffDomain ----------------------------- The workflow of diffDomain is illustrated down below. The goal is to test if a TAD identified in one biological condition has structural changes in another biological condition. The core of diffDomain is formulating the problem as a hypothesis testing problem where the null hypothesis is that the TAD doesn’t undergo significant structural reorganization at later condition. The input are Hi-C contact matrices of the TAD region in the two biological conditions (*A*). The Hi-C contact matrices are log-transformed to adjust for the exponential decay of Hi-C contacts between chromosome bins with increased distances. Their entry-wise difference is calculated (*B*). The difference matrix *D* is normalized by iteratively standardizing its *k*-off diagonal parts, *-N+2 <= k <= N-2*, adjusting absolute differences in contact frequencies due to different sequencing depths in the two biological conditions (*C*). Note that, standardization is TAD-specific. Each TAD has its own parameters that are only estimated from its contact matrices in a pair of biological conditions. Intuitively, if a TAD is not significantly reorganized, normalized *D* would resemble a random matrix with white noise entries, enabling us to borrow theoretical results in random matrix theory. Indeed, normalized *D* is a generalized Wigner matrix (D), a well studied high-dimensional random matrices. | Its largest singular value is proved to be fluctuating around 2 under the null hypothesis. Armed with the fact, diffDomain reformulates the reorganized TAD identification problem into a hypothesis testing problem: | 1. H0: the largest singular value equals to 2; | 2. H1: the largest singular value is greater than 2. | For a user given set of TADs, *P* values are adjusted for multiple comparisons using *BH* method as default. | Once we identify the subset of reorganized TADs, we classify them into six subtypes to aid biological analysis and interpretations. Installation instructions ------------------------- diffDomain is tested on MacOS & Linux (Centos). Dependences ----------- diffDomain-py3 is dependent on - Python 3 - hic-straw 1.3.1 - TracyWidom - pandas - numpy - docopt -tqdm - matplotlib - statsmodels Installation ------------ Download diffDomain source package by running following command in a terminal: :: git clone https://github.com/Tian-Dechao/diffDomain.git or : :: pip install diffDomain-py3 Get started with example usage ============================== We downloaded data `GEO:GSE63525 <https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63525>`__ from Rao et al `(2014) <https://www.sciencedirect.com/science/article/pii/S0092867414014974>`__ for standalone example usage of diffDomain. Example data saved in ``<data/>``: 1. GM12878 TADs. 2. GM12878 combined Hi-C data on Chr1 that is extracted by `Juicebox <https://github.com/aidenlab/Juicebox>`__ with resolution at 10 kb and normalization method at KR. The produced Hi-C data is 3-column: column 1 and column 2 are chromosomal bins, column 3 is KR normalized contact frequencies between the two bins. 3. K562 combined Hi-C data on Chr1. Settings are the same as GM12878. Testing if one TAD is reorganized --------------------------------- In this example, we tested the GM12878 TAD that is reorganized in K562 (Chr1:163500000-165000000, `Ref <http://dx.doi.org/10.1016/j.molcel.2017.07.022>`__). Data are saved in ``<data/single-TAD/>``. Running the command - Usage: scriptname dvsd one <chr> <start> <end> <hic0> <hic1> [options] :: python diffdomain/diffdomains.py dvsd one 1 163500000 165000000 data/single-TAD/GM12878_chr1_163500000_165000000_res_10k.txt data/single-TAD/K562_chr1_163500000_165000000_res_10k.txt --reso 10000 --ofile res/chr1_163500000_165000000.txt diffDomain also provide visualization function to visualize Hi-C matrices side-by-side. - Usage: scriptname visualization <chr> <start> <end> <hic0> <hic1> [options] Figure are saved in ``<res/images/>``. :: python diffdomain/diffdomains.py visualization 1 163500000 165000000 data/single-TAD/GM12878_chr1_163500000_165000000_res_10k.txt data/single-TAD/K562_chr1_163500000_165000000_res_10k.txt --reso 10000 --ofile res/images/side_by_side Note: in this example, there is no need to do multiple comparison adjustment. Multiple comparisons adjustment by *BH* will be demonstrated in the next example. Identifying the reorganized TADs on a 50 Mb region (Chr1:1-50,000,000) ---------------------------------------------------------------------- In this example, multiple comparison adjustment is requried to adjust the *P*-values. chr1_50M_domainlist are saved in ``<data/TADs_chr1/>``. - Usage: scriptname dvsd multiple <hic0> <hic1> <bed> [options] :: python diffdomain/diffdomains.py dvsd multiple data/TADs_chr1/chr1_50M_GM12878.h5 data/TADs_chr1/chr1_50M_K562.h5 data/TADs_chr1/GM12878_chr1_50M_domainlist.txt --reso 10000 --ofile res/temp/GM12878_vs_K562_chr1_50M_temp.txt The function pydiff.diffdomain_multiple will return the dataframe of result_mul. - Adjusting multiple comparisons by *BH* method (default, Optional parameters: *fdr_by*, *bonferroni*, *holm*, *hommel* etc.) and Filtering out reorganized TADs with *BH < 0.05* - Usage: scriptname adjustment <method> <input> <output> :: python diffdomain/diffdomains.py adjustment fdr_bh res/temp/GM12878_vs_K562_chr1_50M_temp.txt res/GM12878_vs_K562_chr1_50M_adjusted_filter.tsv --filter true For interactive integrative analysis, we recommend using the `Nucleome Browser <http://www.nucleome.org/>`__. Example visualization outputs are shown below. .. figure:: /figures/TADs_chr1.png :alt: reorganized TADs on chr1 reorganized TADs on chr1 Identifying GM12878 TADs that are reorganized in K562, using all TADs. ---------------------------------------------------------------------- Data is using Amazon. - Identify TADs in multiple chromosomes simultaneously. :: python diffdomain/diffdomains.py dvsd multiple https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic https://hicfiles.s3.amazonaws.com/hiseq/k562/in-situ/combined.hic data/GSE63525_GM12878_primary+replicate_Arrowhead_domainlist.txt --ofile res/temp/temp.txt - MultiComparison adjustment. :: python diffdomain/diffdomains.py adjustment fdr_bh res/temp/GM12878_vs_K562_chr1_50M_temp.txt res/adjusted_TADs2.txt - optional parameter **[–filter]**, Filtering out reorganized TADs with *BH < 0.05*. :: python diffdomain/diffdomains.py adjustment fdr_bh res/temp/GM12878_vs_K562_chr1_50M_temp.txt res/reorganized_TADs_GM12878_K562.tsv --filter true The final output is saved to ``<res/reorganized_TADs_GM12878_K562.tsv>``. - Classification of TADs Running the command: :: python diffdomain/classificattion.py -d adjusted_TADs2.txt -t GSE63525_K562_Arrowhead_domainlist.txt Contact information =================== More information please contact Dunming Hua at huadm@mail2.sysu.edu.cn, Ming Gu at guming5@mail2.sysu.edu.cn or Dechao Tian at tiandch@mail.sysu.edu.cn.

نیازمندی

مقدار	نام
==1.3.1	hic-straw
-	TracyWidom
-	pandas
-	numpy
-	docopt
-	statsmodels
-	tqdmseaborn
-	matplotlib
-	h5py

نحوه نصب

نصب پکیج whl diffDomain-py3-0.1.9:

pip install diffDomain-py3-0.1.9.whl

نصب پکیج tar.gz diffDomain-py3-0.1.9:

pip install diffDomain-py3-0.1.9.tar.gz