rpkmforgenes protocols

rpkmforgenes statistics

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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 in pipelines

 (11)
2018
PMCID: 5825159
PMID: 29432416
DOI: 10.1371/journal.pgen.1007224

[…] 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 […]

2017
PMCID: 5435343
PMID: 28545064
DOI: 10.1371/journal.pone.0177938

[…] sequence alignment with the reference genome sequences was performed using tophat 1.3.1 []. the unique mapped reads were used in subsequent analyses., for gene expression analysis, the python script rpkmforgenes.py (last modified 13 november, 2014) was used to estimate the expression level (relative abundance) of specific transcripts expressed using the rpkm (reads per kilobase per million reads […]

2017
PMCID: 5578184
PMID: 28820494
DOI: 10.3390/ijms18081796

[…] model per million mapped reads according to mortazavi et al. []) was carried out exclusively with uniquely mapped read pairs using gencode annotation v22 (ensembl release 80) with the python script “rpkmforgenes.py” (http://sandberg.cmb.ki.se/rnaseq/). identification of differentially expressed genes (degs) was done using bioconductor package edger (version 3.4.2, […]

2017
PMCID: 5585943
PMID: 28874114
DOI: 10.1186/s12864-017-4097-4

[…] 0.4.12) with default settings []. a summary of all analyzed samples for rna-seq including sequencing depth and mapping statistics is listed in additional file : table st1. downstream quantification (rpkmforgenes.py, http://sandberg.cmb.ki.se/rnaseq/) of genes in raw read counts as well as rpkm (= reads per kilobase of exon model per million mapped reads according to mortazavi et al. []) […]

2017
PMCID: 5638248
PMID: 29023454
DOI: 10.1371/journal.pone.0184438

[…] 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 […]


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rpkmforgenes in publications

 (13)
PMCID: 5825159
PMID: 29432416
DOI: 10.1371/journal.pgen.1007224

[…] 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 […]

PMCID: 5677350
PMID: 29134197
DOI: 10.1126/sciadv.1701679

[…] 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 […]

PMCID: 5869067
PMID: 28948974
DOI: 10.1038/mp.2017.173

[…] 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 […]

PMCID: 5578184
PMID: 28820494
DOI: 10.3390/ijms18081796

[…] model per million mapped reads according to mortazavi et al. []) was carried out exclusively with uniquely mapped read pairs using gencode annotation v22 (ensembl release 80) with the python script “rpkmforgenes.py” (http://sandberg.cmb.ki.se/rnaseq/). identification of differentially expressed genes (degs) was done using bioconductor package edger (version 3.4.2, […]

PMCID: 5675097
PMID: 29170757
DOI: 10.1002/btm2.10062

[…] at university of wisconsin‐madison. the resulting sequence reads were mapped to the human genome (hg19) using hisat, and the refseq transcript levels (rpkms) were quantified using the python script rpkmforgenes.py. hierarchical clustering of whole transcripts was then plotted using gene‐e. pca was performed using pls toolbox 8.1 (eigenvector technologies). the whole transcripts […]


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

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