|
bwakit
|
public |
A self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping
|
2024-07-02 |
|
mintie
|
public |
Method for Identifying Novel Transcripts and Isoforms
using Equivalence classes, in cancer and rare disease.
|
2024-07-02 |
|
r-sigminer
|
public |
Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff, et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
|
2024-07-01 |
|
syngap
|
public |
SynGAP: Synteny-based Gene structure Annotation Polisher
|
2024-07-01 |
|
gangstr
|
public |
GangSTR is a tool for genome-wide profiling tandem repeats from short reads.
|
2024-06-28 |
|
tetrimmer
|
public |
TETrimmer is designed to replace and assist TE manual curation.
|
2024-06-28 |
|
bohra
|
public |
Pipeline for analysing Illumina data for microbiological public health.
|
2024-06-28 |
|
rnaquast
|
public |
rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
|
2024-06-25 |
|
idr
|
public |
The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility.
|
2024-06-25 |
|
tandem-genotypes
|
public |
Find tandem repeat length changes, from "long" DNA reads aligned to a genome
|
2024-06-25 |
|
spapros
|
public |
Probe set selection for targeted spatial transcriptomics.
|
2024-06-24 |
|
snakemake-storage-plugin-zenodo
|
public |
A Snakemake storage plugin for reading from and writing to zenodo.org
|
2024-06-24 |
|
artic-tools
|
public |
A set of tools for working with the ARTIC bioinformatic pipeline.
|
2024-06-21 |
|
concoct
|
public |
Clustering cONtigs with COverage and ComposiTion
|
2024-06-21 |
|
bioframe
|
public |
Pandas utilities for tab-delimited and other genomic files
|
2024-06-20 |
|
usearch
|
public |
USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
|
2024-06-19 |
|
ciri-full
|
public |
Full length circRNA reconstruction and quantification using BSJ and reverse overlap (RO) features.
|
2024-06-19 |
|
seqverify
|
public |
Seqverify analyzes whole genome sequencing data for gene-editing verification.
|
2024-06-18 |
|
deepmicroclass
|
public |
DeepMicroClass, a deep learning based contig prediction tool
|
2024-06-18 |
|
clever-toolkit
|
public |
The clever toolkit (CTK) is a suite of tools to analyze next-generation sequencing data and, in particular, to discover and genotype insertions and deletions from paired-end reads.
|
2024-06-18 |
|
r-circrnafull
|
public |
An R package for reconstruction of full length circRNA sequence using chimeric alignment information
|
2024-06-18 |
|
jccirc
|
public |
circRNA assembler through integrated junction contigs
|
2024-06-17 |
|
pyplink
|
public |
Python module to read binary Plink files.
|
2024-06-17 |
|
r-dsb
|
public |
Normalizing and denoising protein expression data from droplet-based single cell profiling
|
2024-06-17 |
|
pypgx
|
public |
A Python package for pharmacogenomics research
|
2024-06-16 |
|
fuc
|
public |
Frequently used commands in bioinformatics
|
2024-06-15 |
|
r-tinyarray
|
public |
Gene Expression Omnibus(GEO) and The Cancer Genome Atlas(TCGA) are common bioinformatics public databases. We integrate the regular analysis and charts for expression data, to analyze and display the data concisely and intuitively.
|
2024-06-14 |
|
nanomath
|
public |
A few simple math function for other Oxford Nanopore processing scripts
|
2024-06-14 |
|
autometa
|
public |
Automated extraction of genomes from shotgun metagenomes
|
2024-06-14 |
|
tcfinder
|
public |
A lightweight tool to find clusters of samples within a phylogeny.
|
2024-06-14 |
|
pbcopper
|
public |
Core C++ library for data structures, algorithms, and utilities
|
2024-06-14 |
|
cosap
|
public |
COSAP - Comparative Sequencing Analysis Platform
|
2024-06-14 |
|
humann
|
public |
HUMAnN: The HMP Unified Metabolic Analysis Network, version 3
|
2024-06-13 |
|
metagraph
|
public |
Ultra Scalable Framework for DNA Search, Alignment, Assembly
|
2024-06-13 |
|
ngsderive
|
public |
Backwards derive attributes from NGS data
|
2024-06-13 |
|
dinopy
|
public |
DNA input and output library for Python and Cython. Includes reader and writer for FASTA and FASTQ files, support for samtools faidx files, and generators for solid and gapped q-grams (k-mers).
|
2024-06-13 |
|
jcvi
|
public |
Python utility libraries on genome assembly, annotation, and comparative genomics
|
2024-06-13 |
|
physiofit
|
public |
Calculate extracellular fluxes from metabolite concentrations and biomass data
|
2024-06-13 |
|
bamsurgeon
|
public |
Tools for adding genomic variants to BAM/SAM/CRAM files. Can be used to test variant callers.
|
2024-06-13 |
|
deepblast
|
public |
Neural Networks for Protein Sequence Alignment.
|
2024-06-13 |
|
genomelake
|
public |
Simple and efficient random access to genomic data for deep learning models.
|
2024-06-12 |
|
genometools-genometools
|
public |
GenomeTools genome analysis system.
|
2024-06-12 |
|
mmlong2
|
public |
An all-in-one genome-centric metagenomics workflow using long reads
|
2024-06-12 |
|
sortmerna
|
public |
SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads.
|
2024-06-12 |
|
firecloud
|
public |
API and CLI for Broad Institute's Firecloud workspace/workflow management service.
|
2024-06-12 |
|
perl-getopt-long
|
public |
Module to handle parsing command line options
|
2024-06-12 |
|
ngs-smap
|
public |
SMAP is an analysis tool for stack-based NGS read mapping
|
2024-06-12 |
|
rlpipes
|
public |
A standardized R-loop-mapping pipeline
|
2024-06-12 |
|
pyranges
|
public |
Performant Pythonic GenomicRanges
|
2024-06-12 |
|
tbpore
|
public |
Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data
|
2024-06-12 |
