Stars
Differential expression analysis for single-cell RNA-seq data.
让我们以刷LeetCode题目的形式，来编程解决生物信息学问题吧，Come on
TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact o…
“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau
SALSA: A tool to scaffold long read assemblies with Hi-C data
Earl Grey: A fully automated TE curation and annotation pipeline
RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
Modified version of Alphafold to divide CPU part (MSA and template searching) and GPU part. This can accelerate Alphafold when predicting multiple structures
Chromosome-level scaffolding using multiple references
snipit: summarise snps relative to your reference sequence
pbsv - PacBio structural variant (SV) calling and analysis tools
Tools for manipulating biological data, particularly multiple sequence alignments
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
FAN-C: Framework for the ANalysis of C-like data
Extract 3D contacts (.pairs) from sequencing alignments
An imagemagick-like frontend to Biopython SeqIO
Detecting genome structural variants with deep learning in single molecule sequencing
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like…
Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.
My solution to Bioinformatics Specialization (Finding Hidden Messages in DNA; Genome Sequencing; Comparing Genes, Proteins, and Genomes; Molecular Evolution; Genomic Data Science and Clustering; Fi…
PASTA (Practical Alignment using SATe and Transitivity)
Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.
Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
Calculate summary statistics and manipulate multiple sequence alignments
Python package and CLI for whole-genome duplication related analyses. **This package is deprecated in favor of** https://github.com/heche-psb/wgd.
software for UCE (and general) phylogenomics