Bioinformatics data analysis and visualization toolkit

• 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

Bioinformatics data analysis and visualization toolkit

v0.9 has the following updates and changes (July 28, 2020)

• gene expression raw count normalization class added as 'analys.norm'
• CPM and RPKM normalization function added under 'analys.norm' class
• Sugarcane gene expression dataset added (Bedre et al., 2019)
• In volcano, 'ma', and involcano plots, checks for lfc_thr, counts, and pv_thr added
• legend labels, position, and figname parameters added in volcano plot
• utility to check the non-numeric values added for ma, volcano and involcano
• plotlegend parameter added to ma
• the parameter for log fold change threshold lines added in ma plot
• legend labels, position, and figname parameters added in ma plot
• tsneplot added for t-SNE visualization
• in bardot drop NA value function added to ignore missing values to plot dots
• scRNA-seq dataset added (PBMC and Arabidopsis root cells)
• fasta_reader and rev_com moved to newly created fasta class
• tsneplot and vcf_anot initialized for future release
• more parameters added in biplot (cluster coloring, datapoints)
• figname added in hmap
• ma function updated for absolute expression counts
• svg figures added
• pca function will be deprecated in future release
• 2D and 3D loadings plot, biplot and scree plot functions added under the
  cluster class for PCA
• programmatic access to iris and cotton dataset added
• pca function will be deprecated in future release

Bioinformatics data analysis and visualization toolkit

v0.8 has the following updates and changes

• GFF3 to GTF file conversion utility added and updated under class gff
• In Manhatten plot (visuz.marker.mhat), the labeling issue with markernames parameter corrected (see issue # 4 on GitHub for details;)
• gstyle parameter added in Manhatten plot for box style annotation
• splitvcf function added for splitting VCF file into individual VCF files for each chromosome
• mergevcf moved to analys.marker class
• reg_lin function updated for multiple regression
• degree of freedom fixed for t-test for regression coefficients
• VIF calculation for MLR updated
• functions fastq_reader and fqreadcounter moved to fastq class

Bioinformatics data analysis and visualization toolkit

v0.7 has the following updates and changes

• split_fastq function added for splitting individual (left and right) paired-end fastq files from single
  interleaved paired-end file
• GFF3 to GTF file conversion utility added under class gff
• two-sample and Welch's t-test updated for CI and alpha parameter added
• module termcolor removed
• Programmatic access of dataset for ttsam added

Bioinformatics data analysis and visualization toolkit

v0.6 has the following updates and changes

• Programmatic access of dataset added (class get_data)
• More features for figures added (figtype, axtickfontsize, axtickfontname, axxlabel, axylabel, xlm, ylm,
  yerrlw, yerrcw)
• In volcano plot, the typo for xlabel corrected (-log2(FoldChange) to log2(FoldChange))
• help will be deprecated in future release
• VIF calculation for MLR updated
• adjustText removed

Bioinformatics data analysis and visualization toolkit

v0.5

v0.5 has the following updates and changes

• Linear regression analysis added in analys.stat class
• volcano, involcano, ma and heatmap functions moved to new visuz.gen_exp class
• In volcano, parameters for new box type labeling and threshold grid lines added
• corr_mat updated for new colormaps and moved to stat class
• To visualize the graph in the console itself (e.g. Jupyter notebook), show parameter added
• Pandas dataframe input added for volcano, involcano, corr_mat, ma, ttsam, and chisq
• ttsam and chisq moved to analys.stat class
• graph control parameters added for volcano, involcano, ma, and heatmap
• documentation can also be accessed at https://reneshbedre.github.io/blog/howtoinstall.html
• help will be deprecated in a future release
• fixed the NumPy bug in visuz.stat.bardot. The int cast added to generate the number of samples, which does not accept
  float (See details of NumPy bug: numpy/numpy#15345)

Bioinformatics data analysis and visualization toolkit

v0.4 has the following updates and changes

function analyis.format.fq_qual_var() added for detecting the FASTQ quality encoding format
help module added command-line help message
class fastq added for FASTQ related functions

Bioinformatics data analysis and visualization toolkit

v0.3 has the following updates and changes

1. bar-dot plot function added
2. command-line help message class added