r-make protocols

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r-make specifications

Information


Unique identifier OMICS_05651
Name r-make
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data RNA sequences
Output data Aligned reads, SNP calls, list of indels
Output format FASTQ, STATS, BAM
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Requirements
Make, CMake, GCC, Perl, R, Star, Bamtools, Bedtools Fastx toolkit, Image magick
Maintained Yes

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Documentation


r-make in pipeline

2016
PMCID: 4938719
PMID: 27322744
DOI: 10.1038/nm.4125

[…] nextera xt kit was used for library preparation prior to 100 bp paired-end sequencing on the hiseq 2500 (illumina, inc.) platform. see for sequencing statistics. data analysis was performed using r-make (http://physiology.med.cornell.edu/faculty/mason/lab/r-make/) for quality control, alignment and gene expression quantification., deseq2 was used for differential gene expression analysis […]


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r-make in publications

 (12)
PMCID: 5821318
PMID: 29466446
DOI: 10.1371/journal.pone.0191436

[…] the snpc is clear, but the density of the msn axons, their heterogeneity, and expression of cb1-r on glutamatergic and interneuron terminals that might contribute to the immunoreactivity for cb1-r make it difficult to assign all cb1-rs to a specific axon population in the striosomes., to confirm the source of cb1-r-positive axons in the striosomes, we turned to cre-mediated membrane tdtomato […]

PMCID: 5795819
PMID: 29361781
DOI: 10.3390/s18010315

[…] increasing the value of r results in more conservative control actions, as the requested setpoint value is closer to the current controlled variable value. on the other hand, smaller values of r make the control actions more aggressive, so that the extra distance to reach the requested setpoint is traversed., the performance of neural controllers can be affected negatively by modeling […]

PMCID: 5203714
PMID: 28038678
DOI: 10.1186/s13059-016-1118-6

[…] called seqc) aligned a subset of 1720 universal human reference rna and human brain reference rna samples [] of the 21,504 samples we considered using three different protocols: ncbi magic [], r-make (which uses star []) and subread []. junctions called by rail-rna are compared with junctions called by seqc across the subset in fig. . of junctions found by rail-rna in at least 80 seqc […]

PMCID: 5168849
PMID: 27993156
DOI: 10.1186/s13062-016-0169-7

[…] aceview genes have been assessed by selected tools representing the state of the art in expression profiling analysis. expression estimates are represented in the form of read count equivalents. r-make (based on star) [] and subread [] performs an alignment of sequenced reads to the genome, followed by counting reads that fall into known gene regions. the popular tophat2 tool [] […]

PMCID: 4607093
PMID: 26468086
DOI: 10.1186/s13195-015-0147-9

[…] in assessment of memory. our findings suggest that inclusion of non-verbal memory measures will be an important consideration for future trials. it is possible that inherent properties of bvmt-r make it a strong tool in measuring memory function in a dementia clinic setting. for example, participants are scored on both accuracy of form and accuracy of location of their drawings. as such, […]


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