Shekar: A Python Toolkit for Persian Natural Language Processing • Rank 11.4 • Science 93%

Shekar: A Python Toolkit for Persian Natural Language Processing - Published in JOSS (2025)

ANCOMBC • Rank 19.0 • Science 59%

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

NormalyzerDE • Rank 15.2 • Science 59%

Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.

spilterlize_integrate • Rank 3.9 • Science 67%

A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.

qnorm • Rank 12.0 • Science 54%

Fast-ish (and correct!) quantile normalization in Python.

tstoolbox • Rank 4.6 • Science 54%

Command line script and Python library to work with time-series data.

openmc-tally-unit-converter • Rank 8.5 • Science 44%

A Python package that finds and converts OpenMC tally units.

icellr • Rank 16.2 • Science 23%

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).

HiCcompare • Rank 15.5 • Science 23%

Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices

LambertW • Rank 12.5 • Science 26%

LambertW R package: Lambert W x F distributions and Gaussianization for skewed & heavy-tailed data

proBatch • Rank 13.7 • Science 23%

Tools for Batch Effects Diagnostics and Correction

bayNorm • Rank 13.7 • Science 23%

Normalization for single cell RNA-seq data

neurocombat • Rank 12.8 • Science 10%

Harmonization of multi-site imaging data with ComBat (Python)

manorm • Rank 6.8 • Science 13%

A robust model for quantitative comparison of ChIP-Seq data sets.

manorm2-utils • Rank 6.0 • Science 13%

To pre-process a set of ChIP-seq samples and coordinate with MAnorm2 for differential analysis

https://github.com/nsembleai/nsvision • Rank 3.6 • Science 10%

nsvision is the image data pre and post processing and data augmentation library. It provides utilities for working with image data.

groupmap • Science 44%

GroupMap: beyond mean and variance matching for deep learning

PRONE • Science 26%

R Package for preprocessing, normalizing, and analyzing proteomics data

https://github.com/astrojohannes/normalizer • Science 13%

Interactive 1D spectrum normalizer tool using two different spline fitting methods and either user-defined line windows or automated line window selection.

https://github.com/berenslab/umi-normalization • Science 23%

Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology

swansf-datapreprocessing-sampling-notebooks • Science 57%

These notebooks provide a comprehensive workflow, from start to finish, for processing and analyzing the SWAN-SF dataset. They include detailed steps for reading the dataset files, performing full preprocessing, and executing classification.

https://github.com/amazon-science/exponential-moving-average-normalization • Science 10%

PyTorch implementation of EMAN for self-supervised and semi-supervised learning: https://arxiv.org/abs/2101.08482

evonms • Science 31%

https://github.com/brainlesion/preprocessing • Science 49%

preprocessing tools for multi-modal 3D brain imaging

https://github.com/amazon-science/crossnorm-selfnorm • Science 10%

CrossNorm and SelfNorm for Generalization under Distribution Shifts, ICCV 2021

10 • Science 49%

compare two-point UV/Vis spectroscopy read-out with spectral unmixing

text-normalizer • Science 44%

Text normalizer for obtaining a Unicode Normalization Form for URL creation