Infer Splicing Regulator(ISR)

ISR is a Python based tool to infer Key splicing regulator from differential splicing results. Currently, ISR only support the Skipping Exon analysis.

1. Requirement

  (A) python2.x (>Python2.4)

(B) fisher package: https://pypi.python.org/pypi/fisher/0.1.4

(C) pybedtools package: https://pypi.python.org/pypi/pybedtools

(D) Numpy package: http://www.numpy.org/

2. Installation within the folder:

   Python setup.py install

   to install it to other directory

   Python setup.py install --prefix=="PATH of your choise"

3. Usage

3.1 Input requirement ISR support standard MISO (default), MATS and BED format as input.

Note: for MATS output, current version of ISR can only handle SE (Skipped Exon) analysis output.

For BED format, ISR require BED6 format. The Score Column (Column 5), 0 means downregulation, while 1000 means upregulation of skipped exon.

Here is an example (You can find the raw data from github.com/bioliyezhang/ISR/blob/master/examples/1-human-without-direction/input/).

chr17 39976093 39976275 chr17:37229619:37229801:hnRNPH.1:PMID19749754 0 +

...

3.2 Database:   The compiled databased for human and mouse can be found in the database folder.

3.3 Specific Examples: 3.3.1 Input as a BED format, Not knowing the Splicing regulator regulation in human   （See examples/1-human-without-direction folder)

  Command line:

python ISR_PATH/ISR_v1.1.py -i hnRNPH_SupTable4_hnRNPH.1_PMID19749754_reference_hg19.txt \
-r hg19_Splicing_SF15_ref_20170205_single.bed -t BED

3.3.2 Input as a MISO format, knowing the Splicing regulator regulation in human    （See examples/2-human-with-direction folder)

Command line:

python ISR_PATH/ISR_v1.1.py -i ALK_RNAi_control_vs_treated.miso_bf.txt \
-r hg19_Splicing_SF24_ref_20170225_combine.bed -e hg19_feedin_regulation_matrix.txt

3.3.3 Input as a BED format, Not knowing the Splicing regulator regulation in mouse (See examples/3-mouse-without-direction folder)

Command line:

python ISR_PATH/ISR_v1.1.py -i ESRP_mm10_ESRP1_PMID27050523_reference.txt \
-r mm10_Splicing_SF5_ref_20170205_single.bed -t BED

The output should be the same as the one located in the output folder for each example.