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VERSIONLOG.md

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v2.0.7 and v2.0.8 has the following updates and changes (November 20, 2021)

  • volcano and involcano functions added to GeneExpression class
  • ma function for MA plot updated and added basemean and p value parameters. basemean parameter is useful for visualizing the results from DESeq2.

v2.0.6 has the following updates and changes (August 18, 2021)

  • New function Fasta.split_seq added in analys module for splitting the sequence into smaller subsequences

v2.0.5 has the following updates and changes (August 16, 2021)

  • New function HtsAna.merge_featureCount added in analys module for merging the counts for all samples obtained from featureCounts

v2.0.4 has the following updates and changes (May 10, 2021)

  • New class Fasta replaced with old fasta
  • Fasta.split_fasta function added in analys module

v2.0.3 has the following updates and changes (April 14, 2021)

  • New class GeneExpression and General added
  • MA plot updated for adding the label names to genes and plot title
  • New theme option added to set new background styles to plots (now work only for MA plot)
  • gene_exp class will be deprecated in future releases

v2.0.2 has the following updates and changes (March 13, 2021)

  • PCA biplot updated for the y scale
  • blood pressure dataset added

v2.0.1 has the following updates and changes (March 11, 2021)

  • Dark theme added for image backgrounds

v2.0.0 has the following updates and changes (March 10, 2021)

  • analys.visuz.cluster.biplot function updated to create the biplot where variables are more than observations

v1.0.9 has the following updates and changes (March 07, 2021)

  • analys.visuz.marker.mhat function updated to handle the Fst values for Manhattan plot
  • Boolean log-scale parameter added for choice of minus log10 conversion of p values
  • New marker dataset with Fst values added. This dataset is provided by the Vincent Appiah, which is downloaded from the Pf3K Project (pilot data release 5). This dataset can be accessed using analys.get_data('fst').data.

v1.0.8 has the following updates and changes (February 14, 2021)

  • Function for regression metrics added (bioinfokit.analys.stat.reg_metric)
  • It calculates Root Mean Square Error (RMSE), Mean squared error (MSE), Mean absolute error (MAE), and Mean absolute percent error (MAPE) from regression fit

v1.0.7 has the following updates and changes (January 30, 2021)

  • Plant species richness dataset added for regression analysis

v1.0.6 has the following updates and changes (January 29, 2021)

  • Individual log fold change and p value cutoff added for volcano and inverted volcano plot (bioinfokit.visuz.gene_exp.volcano and bioinfokit.visuz.gene_exp.involcano)

v1.0.5 has the following updates and changes (December 22, 2020)

  • analys.gff.gff_to_gtf function updated to handle dot value for phase in CDS features

v1.0.4 has the following updates and changes (November 22, 2020)

  • `Breast Cancer Wisconsin (Diagnostic) Data Set added
  • visuz.stat.roc function added for visualizing the ROC

v1.0.3 has the following updates and changes (November 06, 2020)

  • 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

v1.0.2 has the following updates and changes (October 26, 2020)

  • 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

v1.0.1 has the following updates and changes (October 24, 2020)

  • 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

v1.0.0 has the following updates and changes (October 10, 2020)

  • genFam enrichment analysis function added (bioinfokit.analys.genfam.fam_enrich)
  • genfam test added

v0.9.9 has the following updates and changes (October 04, 2020)

  • Tukey HSD test added to perform multiple pairwise comparisons (bioinfokit.analys.stat.tukey_hsd)

v0.9.8 has the following updates and changes (September 25, 2020)

  • 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

v0.9.7 has the following updates and changes (September 18, 2020)

  • seqcov moved to fastq class
  • sra_db function added under fastq class for batch download of FASTQ files from NCBI SRA database

v0.9.6 has the following updates and changes (August 22, 2020)

  • 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)

v0.9.5 has the following updates and changes (August 14, 2020)

  • In chi-squared test, the sum of probabilities is rounded to 10 for exact sum in case of floats

v0.9.4 has the following updates and changes (August 13, 2020)

  • 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

v0.9.3 has the following updates and changes (August 08, 2020)

  • 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

v0.9.2 has the following updates and changes (July 30, 2020)

  • The manhatten plot updated to add the lables in sorted order for numerical strings
  • The manhatten plot updated to add figname option

v0.9.1 has the following updates and changes (July 30, 2020)

  • TPM normalization function added

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

  • RPKM normalization function added

v0.8.9 has the following updates and changes (July 28, 2020)

  • gene expression raw count normalization class added as 'analys.norm'
  • CPM normalization function added

v0.8.8 has the following updates and changes (July 02, 2020)

  • check for lfc_thr and pv_thr added

v0.8.7 has the following updates and changes (July 01, 2020)

  • 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

v0.8.6 has the following updates and changes (June 27, 2020)

  • the parameter for log fold change threshold lines added in MA plot
  • legend labels, position, and figname parameters added in MA plot

v0.8.5 has the following updates and changes (June 22, 2020)

  • 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)

v0.8.4 has the following updates and changes (June 17, 2020)

  • 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

v0.8.3 has the following updates and changes (June 03, 2020)

  • ma function updated for absolute expression counts
  • svg figures added
  • pca function will be deprecated in future release

v0.8.1 and v0.8.2 has the following updates and changes (May 31, 2020)

  • 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

v0.8 has the following updates and changes (May 24, 2020)

  • GFF3 to GTF file conversion utility added and updated under class gff

v0.7.3 has the following updates and changes (May 14, 2020)

  • In manhatten plot (visuz.marker.mhat), the labeling issue with markernames parameter corrected (see issue # 4 on github for details; thanks to mkirchler for reporting)
  • gstyle parameter added in manhatten plot for box style annotation

v0.7.2 has the following updates and changes (May 08, 2020)

  • splitvcf function added for splitting VCF file into individual VCF files for each chromosome
  • mergevcf moved to analys.marker class

v0.7.1 has the following updates and changes (April 24, 2020)

  • 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

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

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

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 labelling and threshold grid lines added
  • corr_mat updated for new colormaps and moved to stat class
  • To visualize the graph in 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 future release
  • fixed the numpy bug in visuz.stat.bardot. The int cast added to generate number of samples, which does not accept float (See details of numpy bug: numpy/numpy#15345)

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

v0.3 has the following updates and changes

  • bar-dot plot function added
  • command-line help message class added
  • DOI