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rpkmforgenes specifications

Information


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

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Publication for rpkmforgenes

rpkmforgenes citations

 (27)
library_books

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

2018
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 […]

call_split

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

2017
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 […]

call_split

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

2017
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 […]

library_books

Polysome profiling in small tissue samples

2017
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) […]

call_split

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

2017
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. […]

call_split

A Upf3b mutant mouse model with behavioral and neurogenesis defects

2017
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 […]

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

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