Irtools

Latest version: v1.2.2.1

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1.2.2.1

**Quant:**
- Removed outdated BED implementation

**Miscellaneous:**
- Added tutorial for new IRTools users

1.2.1.1

**Depedencies:**
- Added bx-python installation as requirement

**Miscellaneous:**
- Deleted unused directories/files

1.2.1.0

**Diff:**

- Changed functionality to run analysis based on IR quantification result files from 'IR quant' run rather than running quantification within the method

1.2.0.1

**Diff:**

- Fixed error where FDR values all reported 'nan'

1.2.0.0

**Dependencies:**

- Updated python version requirement from 2 → 3.6.9 or above
- Updated HTSeq version requirement from 0.6.1 → 0.13.5 or above
- Python 3.7 or above is required to run HTSeq 2.0.1
- Updated pysam version requirement from 0.7.6 → 0.19.1 or above

**Annotation:**

- Updated reading of gtf file in run

**Quant:**

- Updated binary reading of BigWig files in function init_mappability_GenomicArray for IRI analysis
- Updated RSeQC utility from version 2.6.2 → 4.0.0
- Parsed out divide by zero warnings in function output_IRI_gene_level and output_IRI_intron_level
- Note: these warnings do not affect output in any way

**Diff:**

- Removed rMATS utility
- Changed rMATS to utilize t-test for differential IRI/IRC analysis
- Applies BH FDR method through the statsmodels.stats.multitest package
- Removed functions filter_invalid_rows, generate_rmats_input_intron_level, generate_rmats_input_gene_level, run_rmats_intron_level, run_rmats_gene_level from IRI_diff class
- Removed functions filter_invalid_rows, generate_rmats_input_junction_level, generate_rmats_input_intron_level, generate_rmats_input_gene_level, run_rmats_junction_level, run_rmats_intron_level, run_rmats_gene_level from IRC_diff class
- Added functions count_distinct_vals, generate_input_intron_level, generate_input_gene_level, run_analysis_intron_level, run_analysis_gene_level to IRI_diff class
- Added functions count_distinct_vals, generate_input_intron_level, generate_input_gene_level, generate_input_junction_level, run_analysis_intron_level, run_analysis_gene_level, run_analysis_junction_level to IRC_diff class
- Added pre-checks for input length/formatting requirements

**Miscellaneous:**

- Corrected spelling errors
- Deleted repetitive/unused code

1.1.4.8

The initial release of IRTools

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