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Published January 6, 2021 | Version 1.0.5
Software Open

reneshbedre/bioinfokit: Bioinformatics data analysis and visualization toolkit

Authors/Creators

  • 1. Texas A&M AgriLife Research

Description

  • analys.gff.gff_to_gtf function updated to handle dot value for phase in CDS features
  • `Breast Cancer Wisconsin (Diagnostic) Data Set added
  • visuz.stat.roc function added for visualizing the ROC
  • bartlett and levene function added to analys.stat class for checking the ANOVA assumptions for datasets in stacked format
  • tukey_hsd function updated for grouping order
  • Pandas series added as input for fasta.extract_seq function
  • extract_seq function moved to fasta class
  • extract_seq function deprecated from analys
  • visualization for single and multiple statistical bar charts updated for future releases
    • Tukey HSD test updated for interaction effect. Pairwise comparison for interaction effect can be calculated.
  • gff_to_gtf function updated for the GFF3 file for non-coding RNA transcripts. GFF3 files with non-coding transcripts (e.g. from miRBase GFF3) can be converted to GTF
  • genFam enrichment analysis function added (bioinfokit.analys.genfam.fam_enrich)
  • genfam test added
  • Tukey HSD test added to perform multiple pairwise comparisons (bioinfokit.analys.stat.tukey_hsd)
  • new option mrna_feature_name added in analys.gff.gff_to_gtf if the name of the feature (column 3 of GFF3 file) of protein coding mRNA is other than 'mRNA' or 'transcript' (e.g. some GFF3 file has this feature named as protein_coding_gene )
  • dim option added to visuz.cluster.screeplot, visuz.cluster.pcaplot and visuz.cluster.biplot to control the figure size
  • seqcov moved to fastq class
  • sra_db function added under fastq class for batch download of FASTQ files from NCBI SRA database
  • In t-test, the one sample t and paired t-test added
  • Two sample t-test switched to class based method
  • t-test function name changed to ttest from ttsam
  • programmatic access to chi-squared independence test dataset added
  • boxplot removed from t-test
  • 'adjustText' module added in setup.py (issue #12)
  • In chi-squared test, the sum of probabilities is rounded to 10 for exact sum in case of floats
  • chi-squared goodness of fit test added under the stat.chisq
  • chi-squared independence test updated for output as class attributes and mosaic plot removed
  • mergevcf renamed to concatvcf to keep with conventional naming (issue # 9)
  • programmatic access to chi-squared independence test dataset added
  • marker.vcf_anot function updated for tab-delimited text output
  • The error message for volcano, inverted volcano, and MA plot updated when there are no significant or non-significant genes (issue # 7)
  • The vcf_anot function output updated for strand information
  • The manhatten plot updated to add the lables in sorted order for numerical strings
  • The manhatten plot updated to add figname option
  • TPM normalization function added

Files

reneshbedre/bioinfokit-1.0.5.zip

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Additional details

Related works

Is supplement to
https://github.com/reneshbedre/bioinfokit/tree/1.0.5 (URL)