read counts是测序之后每个基因测到的reads数量，可用于做差异分析，因为做差异分析的软件要求输入原始reads...
Star399 master 4Branches Tags Code Repository files navigation README GPL-3.0 license README for RSEM Bo Li(bli28 at mgh dot harvard dot edu) Table of Contents Introduction RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides...
By accepting optional cookies, you consent to the processing of your personal data - including transfers to third parties. Some third parties are outside of the European Economic Area, with varying standards of data protection. See our privacy policy for more information on the use of your perso...
value cutoff (default: 0.05) -o --output -t --thread <number> cpu cores (default: 2) -v --version display GCEN version -h --help print help information examples: ./annotate -g ../sample_data/go-basic.obo -a ../sample_data/gene_go.assoc -n ../sample_data/gene_co_expr.netwo...
RSEM is specifically designed to work well with Bowtie. Thus, we also included this embedded mapping and quantification pipeline. Command-line options for all quantification tools are detailed in Supplementary Note 1. Gene expression normalization RNA-seq data normalization enables inter-sample ...
were completed with the online server AliBaba2.1 using the TRANSFAC 4.0 database. CREs shared across panels are bolded blue. Photo credits:P. textilis, Ákos Lumnitzer;L. semifasciata, Patrick Davis;N. sputatrix, Matej Dolinay;C. viridis, Wolfgang Wüster;C. tigris, Ben Lowe ...
When there is a large difference in the number of genes between major and minor organisms, the normalized expression values for each of the target organisms may need to be clustered separately. Otherwise, the data from the major organism may seed almost all the recovered co-expression clusters ...
We identified that 1,358 genes were significantly differentially regulated in IFITM1 KO cells compared to CAS9/Control cells with a p-value of 0.05, a false discovery rate of 0.05, a fold-change threshold of 2.0 (Fig. 4A). Stringency was enhanced by ensuring FPKM (fragments per kilobase ...
By accepting optional cookies, you consent to the processing of your personal data - including transfers to third parties. Some third parties are outside of the European Economic Area, with varying standards of data protection. See our privacy policy for more information on the use of your perso...
In case of multi-mapping reads, RSEM employs a "rescue" method based on estimated maximum likelihood expression levels, which allows partitioning and distributing portions of a multiread's expression value among all of the contigs to which it maps. When RSEM is run with Trinity-assembled ...