rpkmforgenes statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


rpkmforgenes specifications


Unique identifier OMICS_07378
Name rpkmforgenes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for rpkmforgenes

rpkmforgenes citations


SOX2 regulates common and specific stem cell features in the CNS and endoderm derived organs

PLoS Genet
PMCID: 5825159
PMID: 29432416
DOI: 10.1371/journal.pgen.1007224

[…] rer’s instructions. Sequencing of 50bp single end reads was done using an Illumina Genome Analyzer IIx. Star v2.5 [] was used to align reads to mm9, while gene expression levels were calculated using rpkmforgenes.py []. Differential gene expression was assessed using Deseq2 [], with organ specific genes showing differential expression against all other triplicate samples padj < 0.01 and fold chang […]


Adrenergic receptor agonists induce the differentiation of pluripotent stem cell derived hepatoblasts into hepatocyte like cells

Sci Rep
PMCID: 5711806
PMID: 29196668
DOI: 10.1038/s41598-017-16858-5
call_split See protocol

[…] .8.2 pipeline. The sequence reads were mapped to hg19 reference genes downloaded on 25th April 2014 using Tophat v2.0.14. Calculation of the gene expression values and normalization were performed by RPKMforgenes (10th Dec. 2012), and the expression levels were represented by log2(RPKM+1). A heatmap of gene expressions was generated by heatmap.2 function of the gplots library in R 3.2.1. Principle […]


Directed differentiation of human pluripotent stem cells to blood brain barrier endothelial cells

Sci Adv
PMCID: 5677350
PMID: 29134197
DOI: 10.1126/sciadv.1701679
call_split See protocol

[…] onsin-Madison Biotechnology Center. The resulting sequence reads were mapped to the human genome (hg19) using HISAT49, and the RefSeq transcript levels (FPKMs) were quantified using the Python script rpkmforgenes.py50. A hierarchical clustering of whole transcripts was performed using GENE-E on the log2-transformed gene counts. Distances were computed using one minus Pearson correlation with avera […]


Polysome profiling in small tissue samples

Nucleic Acids Res
PMCID: 5758873
PMID: 29069469
DOI: 10.1093/nar/gkx940

[…] and 4 biological replicates of serum starved HCT-116 p53+/+ and HCT-116 p53−/− cells were mapped to the human reference genome GRCh38 using Bowtie () (settings: –a –m 1 –best –strata –n 2 –l 28). The rpkmforgenes script () was used to quantify gene expression (with options -readCount, -fulltranscript and -onlycoding) based on RefSeq annotation. The reads per kilobase per million mapped read (RPKM) […]


Antifungal defense of probiotic Lactobacillus rhamnosus GG is mediated by blocking adhesion and nutrient depletion

PLoS One
PMCID: 5638248
PMID: 29023454
DOI: 10.1371/journal.pone.0184438
call_split See protocol

[…] from Assembly21 (http://www.candidagenome.org/download/sequence/Assembly21) and annotation files from Grumaz et al. [] as reference database. Gene quantification was calculated with a python script `rpkmforgenes.py´ from the Sandberg laboratory (http://sandberg.cmb.ki.se/rnaseq) at readcount and RPKM level (= reads per kilobase of exon model per million mapped reads, according to Mortazavi et al. […]


A Upf3b mutant mouse model with behavioral and neurogenesis defects

Mol Psychiatry
PMCID: 5869067
PMID: 28948974
DOI: 10.1038/mp.2017.173
call_split See protocol

[…] with an Illumina HiSeq 4000 High-Throughput Sequencing System. Libraries were constructed and reads mapped with the RNA-seq aligner STAR,. Counts for each gene were quantified using the python script rpkmforgenes.py and annotated using the Refseq mm10 genome. Reads were filtered, such that genes without at least one sample with at least 10 raw reads and one RPKM reads were removed from the analysi […]


Looking to check out a full list of citations?

rpkmforgenes institution(s)
Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden

rpkmforgenes reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review rpkmforgenes