pyCRAC statistics

info info

Citations per year


Popular tool citations

chevron_left Motif discovery chevron_right

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?


pyCRAC specifications


Unique identifier OMICS_19144
Name pyCRAC
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Sander Granneman <>

Publication for pyCRAC

pyCRAC citations


An RNA dependent mechanism for transient expression of bacterial translocation filaments

PMCID: 5909449
PMID: 29432565
DOI: 10.1093/nar/gky096

[…] in tree et al. () and deposited at ncbi geo under the accession number gse46118. raw sequence data was aligned to the ehec str. sakai genome (nc_002695.1) using novoalign software and analysed using pycrac software ()., rnas that interact with hfq were identified under conditions known to promote t3s expression in e. coli o157:h7 strains (growth in mem-hepes medium). hfq uv-crosslinking (crac) […]


RNA binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination

PMCID: 5678581
PMID: 29117863
DOI: 10.1186/s12915-017-0444-9

[…] interactions (data not shown). the rna from the t7-trim25/rna complex was isolated using a clip-seq protocol and sequenced on a hiseq platform. data analysis and cluster identification using pycrac [] revealed a significant correlation between three biological replicates, with a correlation coefficient between clusters from 0.94 to 0.96 (additional file : figure s4). a total of 5549 […]


Binding to RNA regulates Set1 function

PMCID: 5654745
PMID: 29071121
DOI: 10.1038/celldisc.2017.40

[…] macherey-nagel, düren, germany) and sequenced using illumina technology (san diego, ca, usa). primers are indicated in ., samples were demultiplexed using the pybarcodefilter script from the pycrac utility suite. subsequently, the 3′ adaptor is clipped with cutadapt and the resulting insert is quality trimmed from the 3′-end using trimmomatic rolling mean clipping (window size=5, minimum […]


High throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast

PMCID: 5620067
PMID: 28959008
DOI: 10.1038/s41467-017-00761-8

[…] libraries were pooled based on concentration and barcoding, and paired-end sequencing was performed on hiseq systems by edinburgh genomics (edinburgh). raw data processing was carried out using the pycrac software package and our chemmodseq pipeline (see data and code availability section below). data from replicate experiments were summed to increase the total coverage. the chemmodseqpipeline […]


The N6 methyladenosine (m6A) forming enzyme METTL3 controls myeloid differentiation of normal and leukemia cells

PMCID: 5677536
PMID: 28920958
DOI: 10.1038/nm.4416
call_split See protocol

[…] in summary, raw miclip reads were trimmed of their 3′ adaptor and demultiplexed. then, pcr-duplicated reads of identical sequences were removed using the script of the pycrac tool suite (version unique reads were mapped with novoalign (v3.02.12) using hg19 as reference genome. further analysis including the identification of cits was performed […]


The m6A pathway facilitates sex determination in Drosophila

PMCID: 5500889
PMID: 28675155
DOI: 10.1038/ncomms15737

[…] flexbar -r read1.fastq -p read2.fastq -f i1.8 –a [adaptor sequences file] --pre-trim-phred 30 -n 20 -s –t [timepoint suffix]; and demultiplexed using from the pycrac software suite using the command: -f [timepoint suffix]_1.fastq -r [timepoint suffix]_2.fastq –b [barcode file]. pcr duplicates in the dataset were removed using […]

Want to access the full list of citations?
pyCRAC institution(s)
Centre for Synthetic and Systems Biology (SynthSys), Kings Buildings, Edinburgh, UK; Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK
pyCRAC funding source(s)
Supported by Wellcome Trust Research and Career Development Grants (097383, 091549), the Medical Research Council and the Wellcome Trust Centre for Cell Biology core grant (092076).

pyCRAC reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review pyCRAC