Find nodes in hierarchical clustering that are statistically significant
☆32Oct 15, 2017Updated 8 years ago
Alternatives and similar repositories for treecut
Users that are interested in treecut are comparing it to the libraries listed below
Sorting:
- python (cython) wrapper for https://github.com/ryanlayer/giggle for fast interval searching of huge datasets.☆15Feb 13, 2018Updated 8 years ago
- Python Optimal Leaf Ordering for Hierarchical Clustering☆21Jun 21, 2017Updated 8 years ago
- ☆15Nov 11, 2019Updated 6 years ago
- An easy to use and comprehensive python package which aids in the analysis and visualization of orthologous genes. 🐵☆28Feb 20, 2026Updated 2 weeks ago
- Python translation of the hybrid dynamicTreeCut method as created by Peter Langfelder and Bin Zhang.☆41Sep 17, 2021Updated 4 years ago
- qtools has helper functions to submit jobs to compute clusters (PBS on TSCC, SGE on oolite) from within Python☆21Sep 20, 2023Updated 2 years ago
- ☆11Mar 13, 2012Updated 13 years ago
- Copy number estimation of highly duplicated sequences☆10Aug 15, 2017Updated 8 years ago
- Python package for cancer early detection based on a model of cancer evolution and circulating tumor DNA (ctDNA) shedding☆13Jan 8, 2021Updated 5 years ago
- Phylogenetic iDentification of Subgenomes☆10Jul 7, 2022Updated 3 years ago
- Percentile-normalization method for correcting batch effects in case-control studies☆12Oct 26, 2019Updated 6 years ago
- Lab notebook for people who like the command line.☆11Jun 19, 2024Updated last year
- Software for comparing contact maps from HiC, CaptureC and other 3D genome data.☆26May 21, 2018Updated 7 years ago
- re-assembly and analysis of the Marine Microbial Eukaryotic Transcriptome Sequencing Project☆14Sep 18, 2018Updated 7 years ago
- ☆13Aug 30, 2023Updated 2 years ago
- Sample an approximate number of reads from a fastq file without reading the entire file☆11Jun 20, 2017Updated 8 years ago
- kvector is a small utility for converting motifs to kmer vectors to compare motifs of different lengths☆10May 29, 2017Updated 8 years ago
- Codes for Vmap1.1 and Vmap3☆11Jan 5, 2026Updated 2 months ago
- De novo lncRNA discovery pipeline, re-write of PLAR in shell and awk☆10Aug 2, 2023Updated 2 years ago
- Easily construct the ML species tree with single-copy gene shared by different species.☆27Oct 26, 2018Updated 7 years ago
- 🌊 Robust workflows for gathering data about your local ocean.☆15Jul 19, 2023Updated 2 years ago
- Python package to query and analyse UniProt☆25Sep 8, 2020Updated 5 years ago
- Guided synteny alignment between duplicated genomes (within specified quota constraint)☆59Sep 5, 2017Updated 8 years ago
- Robust individual and aggregate checksums for nucleotide sequences☆17Updated this week
- A minimal and serverless data pipeline☆13Feb 22, 2022Updated 4 years ago
- profile the repeat landscape in a genome☆16Sep 9, 2014Updated 11 years ago
- Jupyter notebook repository for reproducing analysis in "DNA Methylation Landscape of the Mouse Brain at Single-Cell Resolution"☆14Apr 1, 2020Updated 5 years ago
- Benchmarking variant calling in polyploids☆15Nov 26, 2021Updated 4 years ago
- High-level analysis package for (bio-)informatics☆11Feb 27, 2024Updated 2 years ago
- Multithreaded read analysis☆24Feb 25, 2026Updated last week
- Library for visualising genomic features in Python.☆15May 12, 2017Updated 8 years ago
- String search using the Burrows-Wheeler transform☆19Dec 15, 2019Updated 6 years ago
- Repository for the 2017 Genome Biology publication, "The interplay of demography and selection during maize domestication and expansion"☆17Nov 24, 2020Updated 5 years ago
- Convert sequence IDs between ucsc/refseq/genbank☆16Aug 28, 2018Updated 7 years ago
- ☆18Nov 7, 2025Updated 4 months ago
- Summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)☆18Oct 12, 2025Updated 4 months ago
- A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.☆18Jan 16, 2026Updated last month
- Python bindings to minimap2☆16Sep 18, 2017Updated 8 years ago
- Fork of ricopili for development of pipeline for family-based data☆19Jun 22, 2025Updated 8 months ago