Published January 6, 2021
| Version 1.0.5
Software
Open
reneshbedre/bioinfokit: Bioinformatics data analysis and visualization toolkit
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 ROCbartlett
andlevene
function added toanalys.stat
class for checking the ANOVA assumptions for datasets in stacked formattukey_hsd
function updated for grouping order- Pandas series added as input for
fasta.extract_seq
function extract_seq
function moved tofasta
classextract_seq
function deprecated fromanalys
- 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 inanalys.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 tovisuz.cluster.screeplot
,visuz.cluster.pcaplot
andvisuz.cluster.biplot
to control the figure sizeseqcov
moved tofastq
classsra_db
function added underfastq
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
fromttsam
- 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 toconcatvcf
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
Files
(79.4 kB)
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Additional details
Related works
- Is supplement to
- https://github.com/reneshbedre/bioinfokit/tree/1.0.5 (URL)