769 Open source projects that are alternatives of or similar to micca

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

A robust and fast clustering method for amplicon-based studies

Versatile open-source tool for microbiome analysis

Mapping-Assisted Targeted-Assembly for Metagenomics

VirNet: A deep attention model for viral reads identification

A package for designing compact and comprehensive capture probe sets.

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

Improving genome bins through the combination of different binning programs

No description or website provided.

Distributed Elixir Cluster on Render with libcluster and Mix Releases

Project metadata manager for PEPs in Python

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

Introduction to the Unix Shell for biologists

📊 Identify cell types and pathways affected by genetic risk loci.

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

Curated list of bioinformatics formats and publications

A framework for building (and incrementally growing) graph-based data structures used in hierarchical or DAG-structured clustering and nearest neighbor search

Predict plasmids from uncorrected long read data

Workshop (6 hours): Clustering (Hdbscan, LCA, Hopach), dimension reduction (UMAP, GLRM), and anomaly detection (isolation forests).

A library to build and execute typed scientific workflows

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

Build and maintain multiple custom conda environments all in once place.

Examples using Clustergrammer2 to explore high-dimensional datasets.

Fast motif matching in R

Modelling DNA methylation profiles

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

React rerelease of MSAViewer

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

A fast 23andMe genome text file parser, now superseded by arv

REVOLVER - Repeated Evolution in Cancer

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

GraphBin: Refined binning of metagenomic contigs using assembly graphs

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

BACNET is a Java based platform to develop website for multi-omics analysis

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

Clustering methods in Machine Learning includes both theory and python code of each algorithm. Algorithms include K Mean, K Mode, Hierarchical, DB Scan and Gaussian Mixture Model GMM. Interview questions on clustering are also added in the end.

Zio-Entity, a distributed, high performance, functional event sourcing library

TCyb 2018: Graph learning for multiview clustering

Highly parallel DBSCAN (HPDBSCAN)

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

exploratory and interactive microbiome analyses based on heatmaps

An implementation of the Watset clustering algorithm in Java.

Compare different differential abundance and expression methods

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

Genotyping of segregating mobile elements insertions

A curated list of awesome bioinformatics software.

Monte Carlo Reference-based Consensus Clustering

Machine Learning (EE 5184) in NTU

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

Earl Grey: A fully automated TE curation and annotation pipeline

transparently build CWL and Galaxy XML tool definitions for any script that uses argparse

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

Read DNA sequences from colourful Microsoft Word documents

All things Atlassian and Kubernetes

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

Fast alignment and preprocessing of chromatin profiles

a simple & tiny scrapy clustering solution, considered a drop-in replacement for scrapyd

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Per-base per-nucleotide depth analysis