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Version History

###　[v1.3] -

Component Version MaChIAto: 1.8.4 MaChIAto Aligner: 1.1 collect_MaChIAto_data.py 3.01 MaChIAto Analyzer: 1.0 MaChIAto Reviewer: 1.1

changed

add filter bam file to limit to reads without SA or XA tags (prepare_bam_analysis_each_outcome_pe.sh, prepare_bam_comparing_CRISPResso.sh)

###　[v1.2] -

Component Version MaChIAto: 1.8.4 MaChIAto Aligner: 1.0 collect_MaChIAto_data.py 3.01 MaChIAto Analyzer: 1.0 MaChIAto Reviewer: 1.1

changed

fix to k=2 in kmeans because the other component cannot follow the data with k>2 in MaChIAto Analyzer (ManageAnalysisData-class.R)

###　[v1.1] -

Component Version MaChIAto: 1.8.4 MaChIAto Aligner: 1.0 collect_MaChIAto_data.py 3.01 MaChIAto Analyzer: 1.0 MaChIAto Reviewer: 1.1

added

add a function summerizing the MaChIAto Classification with Unclassified in MaChIAto Reviewer

###　[v1.0] -

Component Version MaChIAto: 1.8.4 MaChIAto Aligner: 1.0 collect_MaChIAto_data.py 3.01 MaChIAto Analyzer: 1.0 MaChIAto Reviewer: 1.0

added

add Dockerfile add filter to process samples listed in the label_sample_type.csv in MaChIAtoReviewer.R add trf409.linux64 to calculate the Repeat feature in Linux in CalcThermo-class.R

fixed

Remove em space in MaChIAtoReviewerFunctions.R add snv.range in RunLocalMutationAnalysis.R collect_MaChIAto_data.py makes output directory if it does not exist deprecated expression of ggplot is changed in MaChIAtoReviewerFunctions.R The detection of LSL was not correct and fixed in CalcThermo-class.R

changed

ggpubr is removed because it is not used in MaChIAto Analyzer

###　Release!!!

###　[v2.0beta] -

Component Version MaChIAto: 1.8.4 MaChIAto Aligner: 1.6.beta collect_MaChIAto_data.py 3.00 MaChIAto Analyzer: beta.1.7.4 MaChIAto Reviewer: beta.2.6

fixed
  • the number of variant shown in the wildtype alignment and barplot is limited in MaChIAto Aligner

###　[v1.9beta] -

added
  • csv data for pie chart contains color code in MaChIAto Aligner
  • all data that is used for plot is exported to the result in MaChIAto Aligner
  • the classification for frameshift variants is available in MaChIAto Aligner
fixed
  • the most of plot data is exported as .csv format in MaChIAto Aligner

###　[v1.8beta] -

added
  • recognition of "Scaffold-incorporated" in Alleles_frequency_table.txt in MaChIAto Classifier.
fixed
  • table with a certain amplicon name can be recognized when CRSIRPEsso2 format is processed in MaChIAto Classifier.
  • some optimization parameters is calculated as float variables in MaChIAto Classifier.
  • result of correlation test can be put out in MaChIAto Analyzer.
changed
  • hybrid-ss-min (OligoArrayAux subset) is installed into conda environment. The path is overwritten in CalcThermo-class.R of MaChIAto Analyzer.

###　[v1.7beta] - 2020-07-27

added
  • MaChIAto Classifier adapted the format of CRISPResso2 Prime Editing mode.
fixed
  • Some errors due to the value of zero and Inf in MaChIAto Reviewer.
changed
  • In knock-out analysis, changes of precise knock-in and impricise knock-in becomes invisible on the box charts in MaChIAto Reviewer.

###　[v1.6beta] - 2020-06-30

fixed
  • plot window of distribution is not defined in MaChIAto Reviewer.
changed
  • The class label that has no read becomes invisible on the pie charts in MaChIAto.

###　[v1.5beta] - 2020-06-14

fixed
  • missing samples included in ignore_list in MaChIAto Reviewer
Changed
  • installation of oligoarrayaux-3.8 for calculation of MEF in MaChIAto Analyzer
  • order of plyr and dplyr when loding library in MaChIAto Analyzer
  • summarize_each() replaced into summarize(across) in MaChIAto Reviewer
Added
  • boxplot of each fearure in MaChIAto Analyzer

###　[v1.5beta] - 2020-05-26

Changed
  • The script of MaChIAto Analyzer is modified to perform calculation of each rate and sample set that user want to observe.
  • The sgRNA and edited homology arm can be used as a calculation target on MaChIAto Analyzer.
  • MaChIAto Analyzer can work without the extra table.
  • MaChIAto Analyzer and Reviewer can analyze single knock-in sample and single/double knock-out sample.
  • The sample with less classified reads will be filtered.

###　[v1.4beta] - 2020-02-25

CrispRVariants instalation with conda did not work. I solved this problem by changing download function.

MaChIAto Classifier version 1.7.1

Changed
  • The input sequecence is converted into upper letter in the parameter checking.

MaChIAto Aligner version 1.4

Changed
  • Pathnames given by user become processed into string with no end-slash
  • All R package depends on package intallation program.

###　[1.0alpha-v1.3beta] - 2020-01-30

I developed Prime Editing analysis mode.

MaChIAto (Classifer) version 1.7.0

Added
  • Prime editing analysis mode
  • Detection of ambiguous reads
  • Piechart of classification
Changed
  • Default paramters was adjusted for new mode
  • Default µHs lengh was changed into 20 bp
  • Order of column in xxx_dataframe.csv

MaChIAto Aligner version 1.3

Changed
  • Method to get sequence in shell scripts

MaChIAto Analyzer version beta.1.5

Changed
  • Filter for samples include NA in the value set is removed because it also lose the available values
Deleted
  • Extra comments

MaChIAto Reviewer version beta2.3

Deleted
  • Codes that only works in local environment of a developer