451 Open source projects that are alternatives of or similar to TypeTE

annotate a VCF with other VCFs/BEDs/tabixed files

C library for high-throughput sequencing data formats

Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model

Earl Grey: A fully automated TE curation and annotation pipeline

Scalable genomic data analysis.

Efficient variant-call data storage and retrieval library using the TileDB storage library.

Haplotype VCF comparison tools

A collection of scripts and notes related to genomics and bioinformatics

Syntax highlighting for computational biology

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

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

Toolset for SV simulation, comparison and filtering

Structural variant toolkit for VCFs

Bayesian genotyper for structural variants

highly-efficient & lightweight mutation signature matrix aggregation

cython + htslib == fast VCF and BCF processing

Method to optimally select samples for validation and resequencing

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

My own tools code for NGS data analysis (Next Generation Sequencing)

MView extracts and reformats the results of a sequence database search or multiple alignment.

A curated list of resources for machine learning for small-molecule drug discovery

A computational library for learning and evaluating biological knowledge graph embeddings

An open-access bioinformatics text

Version 5 of the CAFE phylogenetics software

Feature extraction algorithm for genomic data

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

🎯 Human transcription factor target genes.

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

GWAS summary statistics files QC tool

Compute N50/NG50 and auN/auNG

Genomics data visualization in Python by using matplotlib.

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

Rapid determination of appropriate reference genomes.

WebGL Heatmap Viewer for Big Data and Bioinformatics

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.

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

🍶Genome assembly with short sequence reads

A package for designing compact and comprehensive capture probe sets.

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

Unsupervised domain adaptation method for relation extraction

Ploidy agnostic phasing pipeline and algorithm

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

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

Fast alignment and preprocessing of chromatin profiles

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

Read and write FASTQ and FASTA efficiently from Python

Python API for comprehensive GWAS analysis using GEMMA

SaffronTree: Reference free rapid phylogenetic tree construction from raw read data

Fast hash function for DNA sequences

Assembling the cause of phenotypes and genotypes from NGS data

3D printed sculpture of a DNA molecule, showing my own genome

API for linked biological knowledge

Bioinformatics pipeline for SARS-CoV-2 sequencing at CZ Biohub

Fast and flexible ORF finder

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).

Golang for Bioinformatics

Per-base per-nucleotide depth analysis