随笔分类 -  [25] 生物信息学

计算生物信息学,计算生物学,生物统计学,生物数学,分子生物学,遗传学,医学遗传学
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)
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)
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)
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)
摘要: 阅读全文
posted @ 2021-01-24 19:19 emanlee 阅读(94) 评论(0) 推荐(0)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)