seq1 = "ATAC_Data/ATAC_FQs/SRR891269_2.fastq" ) asBam("ATAC_50K_2_bowtie2.sam")8....
T. et al. CLIPdb: a CLIP-seq database for protein-RNA interactions. BMC Genom. 16, 51 (2015).Yang YC, Di C, Hu B, Zhou M, Liu Y, Song N, et al. CLIPdb: a CLIP-seq database for protein-RNA inter- actions. BMC genomics. 2015; 16:51. doi: 10.1186/s12864-015-1273-2 ...
CLIPdb: a CLIP-seq database for protein-RNA interactions 作者:Yang, Yu-Cheng T.; Di, Chao; Hu, Boqin; Zhou, Meifeng; Liu, Yifang; Song, Nanxi; Li, Yang; Umetsu, Jumpei; Lu, Zhi John* 来源:BMC Genomics, 2015, 16(1): 51. ...
Peak calling tool for CLIP-seq data Installation PEAKachu is available via bioconda and can be installed using conda create -n peakachu peakachu python=3 Alternativaly, PEAKachu can be installed from source $ make readme_rst $ make package $ pip3 install --user dist/PEAKachu-0.2.0....
Conclusion Manually curated metadata and uniformly identified binding sites of publicly available CLIP-seq data sets will be a foundation for further integrative and comparative analyses. With maintained up-to-date data sets and improved functionality, CLIPdb (http://clipdb.ncrnalab.org webcite) will...
内容提示: starBase v2.0: decoding miRNA-ceRNA,miRNA-ncRNA and protein–RNA interactionnetworks from large-scale CLIP-Seq dataJun-Hao Li, Shun Liu, Hui Zhou, Liang-Hu Qu* and Jian-Hua Yang*RNA Information Center, Key Laboratory of Gene Engineering of the Ministry of Education, State Key...
In starBase v2.0, we performed a large-scale integration of public RBP binding sites generated by high-throughput CLIP-Seq technology and provided the most comprehensive RBP data set for various cell types that are presently available. By analyzing millions of Ago and other RBP binding sites, we...
CLIPdb:aCLIP-seqdatabaseforprotein-RNA interactions Yu-ChengTYang 1† ,ChaoDi 1† ,BoqinHu 1† ,MeifengZhou 1 ,YifangLiu 1 ,NanxiSong 1 ,YangLi 1 , JumpeiUmetsu 1,2 andZhiJohnLu 1* Abstract Background:RNA-bindingproteins(RBPs)playessentialrolesingeneexpressionregulationthroughtheir ...
PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP. Installation You can install PureCLIP from Bioconda, from the release tarballs and from source. Bioconda Using Conda with an activated Bioconda channel is the easiest wa...
(RBPs) connect across the whole genome, giving you a glimpse into the networks that manage gene expression. We handle everything: from getting your samples ready and doing the UV cross-linking to immunoprecipitation, high-throughput sequencing, and breaking down the data. This way, you get ...