[25] 生物信息学 - 随笔分类(第3页) - emanlee

分子对接

摘要：分子对接是通过受体的特征以及受体和药物分子之间的相互作用方式来进行药物设计的方法。主要研究分子间(如配体和受体)相互作用,并预测其结合模式和亲合力的一种理论模拟方法.近年来,分子对接方法已成为计算机辅助药物研究领域的一项重要技术。分子对接方法分子对接方法的两大课题是分子之间的空间识别和能量识别。阅读全文

posted @ 2021-03-14 10:20 emanlee 阅读(4812) 评论(0) 推荐(0)

SRA toolkit

摘要：使用SRAdb V2获取SRA数据安装SRAdbV2包install.packages('BiocManager')BiocManager::install('seandavi/SRAdbV2')使用SRAdbV2 首先需要创建一个 R6类-Omicidx library(SRAdbV2)oidx 阅读全文

posted @ 2021-03-08 20:39 emanlee 阅读(369) 评论(0) 推荐(0)

Sequence Read Archive (SRA)

摘要：The Sequence Read Archive (SRA) is an archive for high throughput sequencing data, publically accessible, for the purpose of enhancing reproducibility 阅读全文

posted @ 2021-03-08 20:07 emanlee 阅读(469) 评论(0) 推荐(0)

常用物种拉丁文名称

摘要：Homo sapiens (human，人) Mus musculus (mouse，小鼠) Rattus norvegicus (rat，大鼠) Xenopus laevis (frog，爪蟾) Drosophila melanogaster (fruit fly，果蝇) Caenorhabdit 阅读全文

posted @ 2021-03-06 08:22 emanlee 阅读(38561) 评论(0) 推荐(0)

cytoscape port already in use

摘要：阅读全文

posted @ 2021-01-24 19:19 emanlee 阅读(94) 评论(0) 推荐(0)

IOCMIN: Identification of Conserved Motifs in Networks

摘要：IOCMIN: Identification of Conserved Motifs in Networks IOCMIN: Identification of Conserved Motifs in Networks IOCMIN: Identification of Conserved Moti 阅读全文

posted @ 2020-12-13 08:52 emanlee 阅读(159) 评论(0) 推荐(0)

topGO 精选资料

摘要：topGO http://www.bio-info-trainee.com/699.html https://blog.csdn.net/weixin_43569478/article/details/83743975 https://blog.csdn.net/wt141643/article/d 阅读全文

posted @ 2020-11-16 10:20 emanlee 阅读(257) 评论(0) 推荐(0)

GO结果画图

摘要：R语言画图，参考： http://blog.sina.com.cn/s/blog_1704ff73a0102wtx4.html https://www.yuque.com/shenweiyan/cookbook/nvi8vg https://www.jianshu.com/p/166551f66b4 阅读全文

posted @ 2020-11-08 23:32 emanlee 阅读(446) 评论(0) 推荐(0)

clusterProfiler::enrichGO() is getting very slow

摘要：REF https://www.biostars.org/p/389208/ https://github.com/YuLab-SMU/clusterProfiler/issues/155 https://cran.r-project.org/web/packages/enrichR/vignett 阅读全文

posted @ 2020-11-05 22:27 emanlee 阅读(480) 评论(0) 推荐(0)

clusterProfiler

摘要：clusterProfiler也是通过KEGG API去获取物种对应的pathway注释，对于已有pathway注释的物种，我们只需要知道对应的三字母缩写， clusterProfiler就会联网自动获取该物种的pathway注释信息。在clusterProfiler中，enrichKEGG（KE 阅读全文

posted @ 2020-11-01 21:53 emanlee 阅读(1619) 评论(0) 推荐(0)

a command line protocol for doing ontology/pathway analysis

摘要：In Bioconductor there are many packages that can do that, something like topGO or others. You can look this answer: A: How can I do GO enrichment anal 阅读全文

posted @ 2020-10-30 09:37 emanlee 阅读(98) 评论(0) 推荐(0)

GUPPY 3.1.5 安装

摘要：wget https://mirror.oxfordnanoportal.com/software/analysis/ont-guppy-cpu-3.1.5-1.el7.x86_64.rpmsudo yum install ont-guppy-cpu-3.1.5-1.el7.x86_64.rpmgu 阅读全文

posted @ 2020-09-13 22:51 emanlee 阅读(4452) 评论(0) 推荐(0)

clusterMaker (Cytoscape, MCL cluster) 网络聚类，网络划分子网路，子模块。

摘要：Cytoscape -- apps -- clusterMaker -- MCL cluster. MCL cluster的用法用途：网络聚类，网络划分子网路，子模块。安装插件：选中网络，然后做如下操作新网络会出现在新窗口中。阅读全文

posted @ 2020-08-31 10:45 emanlee 阅读(2696) 评论(2) 推荐(0)

dask

摘要：https://pypi.org/project/dask/ [root@ibiomed lib-dynload]# pip install daskCollecting dask Downloading dask-2.25.0-py3-none-any.whl (834 kB) |████████ 阅读全文

posted @ 2020-08-29 21:39 emanlee 阅读(894) 评论(0) 推荐(0)

nanopolish 安装使用

摘要：https://github.com/jts/nanopolish nanopolish Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate a 阅读全文

posted @ 2020-08-29 21:21 emanlee 阅读(1457) 评论(0) 推荐(0)

h5py

摘要：HDF5 for Python h5py is a thin, pythonic wrapper around the HDF5, which runs on Python 3 (3.6+). Websites Main website: https://www.h5py.org Source co 阅读全文

posted @ 2020-08-29 21:18 emanlee 阅读(405) 评论(0) 推荐(0)

Sam2Tsv 安装使用

摘要：官网 http://lindenb.github.io/jvarkit/Sam2Tsv.html 下载安装 $ git clone "https://github.com/lindenb/jvarkit.git"$ cd jvarkit$ ./gradlew sam2tsv Example $ ja 阅读全文

posted @ 2020-08-29 21:13 emanlee 阅读(575) 评论(0) 推荐(0)

samtools 安装使用

摘要：官网： https://github.com/samtools/samtools https://github.com/samtools/samtools/releases https://github.com/samtools/samtools/blob/develop/INSTALL 安装： w 阅读全文

posted @ 2020-08-29 21:10 emanlee 阅读(2806) 评论(0) 推荐(0)

minimap2安装使用

摘要：官网： https://github.com/lh3/minimap2 https://github.com/lh3/minimap2/releases/tag/v2.17 Download and install: wget https://github.com/lh3/minimap2/rele 阅读全文

posted @ 2020-08-29 20:57 emanlee 阅读(5060) 评论(0) 推荐(0)

pip安装pysam

摘要：pysam - a python module for reading, manipulating and writing genomic data sets. pysam is a lightweight wrapper of the htslib C-API and provides facil 阅读全文

posted @ 2020-08-28 11:11 emanlee 阅读(6895) 评论(0) 推荐(0)

随笔分类 - [25] 生物信息学