Before running any of the scripts, loadcreate_cistarget_databasesconda environment and set thecreate_cistarget_databases_dirvariable to the dir that contains the cloned repo. #Activate conda environment.conda activate create_cistarget_databases#Set ${create_cistarget_databases_dir} variable to path w...
运行create_cisTarget_motif_databases.py cd/home/lwc/scRNA/SCENIC/create_cisTarget_databases ln-s~/scRNA/SCENIC/Rattus_cistarget_database/upstream2000.fa ln-s~/scRNA/SCENIC/Rattus_cistarget_database/pwms_all_motifs/ln-s~/scRNA/SCENIC/Rattus_cistarget_database/motif_list.txt python create_cist...
链接在这cisTarget databases (aertslab.org) cisTarget databases List of databases for the cisTarget family of tools (e.g.RcisTarget,SCENIC/pySCENIC, andcisTopic). To choose the database appropiate for your analysis, start by selecting thespeciesandranking type(i.e. What do you want to analy...
A systematic scanning of nucleic acid databases for DNA elements made of combinations of RGGTCA nuclear receptor half sites, has revealed that identical 19 nucleotide-long motifs composed of two inverted RGGTCA sites with a spacing of 7 nucleotides (IR7), are present upstream of the regions ...
Prostate cancer is the second most commonly diagnosed malignancy among men worldwide. Recurrently mutated in primary and metastatic prostate tumors, FOXA1 encodes a pioneer transcription factor involved in disease onset and progression through both andro
备选方案:直接下载数据库 # Specify database name: feather_database_url='https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc8nr/gene_based/hg19-500bp-upstream-7species.mc8nr.feather' feather_database="${feather_database_url##*/}" # Download database directly...
wget https://resources.aertslab.org/cistarget/databases/sha256sum.txt # curl -O https://resources.aertslab.org/cistarget/databases/sha256sum.txt # Check if sha256 checksum matches for the downloaded database: awk -v feather_database=${feather_database} '$2 == feather_database' sha256su...
{feather_database_url}"Will not apply HSTS.The HSTS database must be a regularandnon-world-writable file.ERROR:could notopenHSTS store at'/home/lxwang/.wget-hsts'.HSTS will be disabled.--2021-04-1410:20:25--https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_...
先运行如下命令下载一个文件 用来检查数据完整性。 # Download sha256sum.txt (with wget or curl):wget https://resources.aertslab.org/cistarget/databases/sha256sum.txt 得到sha256sum.txt 内容如下: image.png 然后把你下载的文件逐个放进data文件去检查。
Create cisTarget databases ℹ️The SCENIC+ public motif collection PWMs can be found athttps://resources.aertslab.org/cistarget/motif_collections/. You can find precomputed databases for human, mouse and fly athttps://resources.aertslab.org/cistarget/. ...