|
rust-ncbitaxonomy
|
public |
A Rust crate for working with a local copy of the NCBI Taxonomy database, which provides utilities for taxonomic filtering.
|
2024-08-09 |
|
parafly
|
public |
Given a file containing a list of unix commands, multithreading is used to process the commands in parallel on a single server. Success/failure is captured, and failed commands are retained and reported.
|
2024-08-09 |
|
cgpbigwig
|
public |
BigWig manpulation tools using libBigWig and htslib
|
2024-08-08 |
|
picrust2
|
public |
PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
|
2024-08-08 |
|
sonicparanoid
|
public |
SonicParanoid: fast, accurate, and comprehensive orthology inference with machine learning and language models
|
2024-08-07 |
|
chewbbaca
|
public |
A complete suite for gene-by-gene schema creation and strain identification.
|
2024-08-06 |
|
irfinder
|
public |
Intron Retention Finder
|
2024-08-06 |
|
fastool
|
public |
A simple and quick tool to read huge FastQ and FastA files (both normal and gzipped) and manipulate them.
|
2024-08-06 |
|
umi_tools
|
public |
Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs)
|
2024-08-05 |
|
bam-readcount
|
public |
bam-readcount generates metrics at single nucleotide positions.
|
2024-08-05 |
|
iqtree
|
public |
Efficient phylogenomic software by maximum likelihood.
|
2024-08-04 |
|
quicksect
|
public |
A cythonized, extended version of the interval search tree in bx
|
2024-08-02 |
|
filtlong
|
public |
Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
|
2024-08-01 |
|
r-ichorcna
|
public |
Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
|
2024-08-01 |
|
sequencetools
|
public |
Tools for population genetics on sequencing data
|
2024-08-01 |
|
sourmash
|
public |
Compute and compare MinHash signatures for DNA data sets.
|
2024-08-01 |
|
rnashapes
|
public |
RNAshape abstraction maps structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features, but disregarding helix lengths. Shape abstraction integrates well with dynamic programming algorithms, and hence it can be applied during structure prediction rather than afterwards. This avoids exponential explosion and can still give us a non-heuristic and complete account of properties of the molecule's folding space.
|
2024-07-31 |
|
perl-json
|
public |
JSON (JavaScript Object Notation) encoder/decoder
|
2024-07-31 |
|
perl-json-xs
|
public |
JSON serialising/deserialising, done correctly and fast
|
2024-07-31 |
|
ntcard
|
public |
Estimating k-mer coverage histogram of genomics data
|
2024-07-25 |
|
links
|
public |
Long Interval Nucleotide K-mer Scaffolder
|
2024-07-25 |
|
morpheus
|
public |
mass spectrometry–based proteomics database search algorithm
|
2024-07-25 |
|
seqtk
|
public |
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format
|
2024-07-24 |
|
entrez-direct
|
public |
Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
|
2024-07-23 |
|
kma
|
public |
KMA is mapping a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.
|
2024-07-23 |
|
pydna
|
public |
Representing double stranded DNA and functions for simulating cloning and homologous recombination between DNA molecules.
|
2024-07-19 |
|
pybedtools
|
public |
Wraps BEDTools for use in Python and adds many additional features.
|
2024-07-19 |
|
nonpareil
|
public |
Estimate average coverage and create curves for metagenomic datasets
|
2024-07-19 |
|
r-ic10
|
public |
Implementation of the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group.
|
2024-07-19 |
|
primer3-py
|
public |
Python bindings for Primer3
|
2024-07-19 |
|
gffcompare
|
public |
GffCompare by Geo Pertea
|
2024-07-18 |
|
fido
|
public |
No Summary
|
2024-07-17 |
|
cancerit-allelecount
|
public |
Support code for NGS copy number algorithms
|
2024-07-17 |
|
bowtie
|
public |
An ultrafast memory-efficient short read aligner
|
2024-07-17 |
|
bwa
|
public |
The BWA read mapper.
|
2024-07-17 |
|
libbigwig
|
public |
A C library for handling bigWig files
|
2024-07-16 |
|
graftm
|
public |
GraftM is a pipeline used for identifying and classifying marker gene reads from metagenomic datasets
|
2024-07-16 |
|
mappy
|
public |
Minimap2 Python binding
|
2024-07-15 |
|
bellmans-gapc
|
public |
A language and compiler for algebraic dynamic programming.
|
2024-07-15 |
|
illumina-interop
|
public |
The Illumina InterOp libraries are a set of common routines used for reading and writing InterOp metric files. These metric files are binary files produced during a run providing detailed statistics about a run. In a few cases, the metric files are produced after a run during secondary analysis (index metrics) or for faster display of a subset of the original data (collapsed quality scores).
|
2024-07-15 |
|
dropseq_tools
|
public |
Package for the analysis of Drop-seq data developed by Jim Nemesh in the McCarroll Lab
|
2024-07-15 |
|
r-rrbgen
|
public |
A lightweight limited functionality R bgen read/write library
|
2024-07-15 |
|
pairix
|
public |
2D indexing on bgzipped text files of paired genomic coordinates
|
2024-07-12 |
|
perl-digest-sha1
|
public |
Perl interface to the SHA-1 algorithm
|
2024-07-12 |
|
skesa
|
public |
Strategic Kmer Extension for Scrupulous Assemblies & Sequence Assembly Using Target Enrichment
|
2024-07-12 |
|
gap2seq
|
public |
Gap2Seq is a tool for filling gaps between contigs in genome assemblies.
|
2024-07-12 |
|
vcftools
|
public |
A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries
|
2024-07-11 |
|
raxml
|
public |
Phylogenetics - Randomized Axelerated Maximum Likelihood.
|
2024-07-11 |
|
xtandem
|
public |
No Summary
|
2024-07-11 |
|
kalign2
|
public |
Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.
|
2024-07-11 |
