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r-cellassign
|
public |
Automated, probabilistic assignment of cell types in scRNA-seq data
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2025-03-25 |
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r-pophelper
|
public |
A set of useful functions for processing admixture proportion files from the population structure analysis softwares STRUCTURE, TESS, ADMIXTURE, BAPS, fastSTRUCTURE etc. The package contains functions to read runs, tabulate runs, summarise runs, plot runs, estimate K using Evanno method, export clumpp files, export distruct files and generate barplots.
|
2025-03-25 |
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readfq
|
public |
A high-speed tool to calculate reads number and total base count in FASTQ file, forked from Li Heng's original version
|
2025-03-25 |
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consel
|
public |
CONSEL calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection
|
2025-03-25 |
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islandpath
|
public |
IslandPath-DIMOB is a standalone software to predict genomic islands in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes.
Genomic islands (GIs) are clusters of genes in prokaryotic genomes of probable horizontal origin. GIs are disproportionately associated with microbial adaptations of medical or environmental interest.
|
2025-03-25 |
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perl-moosex-singleton
|
public |
Turn your Moose class into a singleton
|
2025-03-25 |
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gappa
|
public |
Genesis Applications for Phylogenetic Placement Analysis
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2025-03-25 |
|
ir
|
public |
Program for Calculating the Repetitiveness of DNA Sequences
|
2025-03-25 |
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digestiflow-demux
|
public |
Digestiflow Command Line Client.
|
2025-03-25 |
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digestiflow-cli
|
public |
Command line client for Digestiflow.
|
2025-03-25 |
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r-taxonomizr
|
public |
Functions for assigning taxonomy to NCBI accession numbers and taxon IDs based on NCBI's accession2taxid and taxdump files. This package allows the user to downloads NCBI data dumps and create a local database for fast and local taxonomic assignment.
|
2025-03-25 |
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xpclr
|
public |
Code to compute xp-clr values to detect selection as per Chen, Patterson & Reich 2010.
|
2025-03-25 |
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perl-local-lib
|
public |
create and use a local lib/ for perl modules with PERL5LIB
|
2025-03-25 |
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rust-ncbitaxonomy
|
public |
A Rust crate for working with a local copy of the NCBI Taxonomy database, which provides utilities for taxonomic filtering.
|
2025-03-25 |
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calour
|
public |
exploratory and interactive microbiome analyses based on heatmaps
|
2025-03-25 |
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mirtrace
|
public |
miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq).
Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the
amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine
quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the
composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. It can
also be applied for more specific applications in forensics, food quality control and clinical diagnosis, for instance tracing the
origins of meat products or detecting parasitic microRNAs in host serum.
|
2025-03-25 |
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faststructure
|
public |
A variational framework for inferring population structure from SNP genotype data.
|
2025-03-25 |
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stream_atac
|
public |
STREAM-Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data. Preprocessing steps for single cell atac-seq data.
|
2025-03-25 |
|
perl-test-script
|
public |
Basic cross-platform tests for scripts
|
2025-03-25 |
|
plantcv
|
public |
An image processing package for plant phenotyping.
|
2025-03-25 |
|
perl-probe-perl
|
public |
Information about the currently running perl
|
2025-03-25 |
|
cgat-apps
|
public |
Computational Genomics Analysis Toolkit.
|
2025-03-25 |
|
ivar
|
public |
iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
|
2025-03-25 |
|
sbg-cwl-runner
|
public |
A CWL Runner for SBG platform
|
2025-03-25 |
|
refinem
|
public |
A toolbox for improving population genomes.
|
2025-03-25 |
|
nullarbor
|
public |
Reads to report pipeline for bacterial isolate NGS data
|
2025-03-25 |
|
r-rrbgen
|
public |
A lightweight limited functionality R bgen read/write library
|
2025-03-25 |
|
sample-sheet
|
public |
An Illumina Sample Sheet parsing library
|
2025-03-25 |
|
seqlogo
|
public |
Python port of the R Bioconductor `seqlogo` package
|
2025-03-25 |
|
nemo
|
public |
Individual-based forward-time genetics simulation software
|
2025-03-25 |
|
goslimmer
|
public |
GOSlimmer transforms GO annotations to a slimmed version of GO
|
2025-03-25 |
|
goenrichment
|
public |
GOEnrichment analyses a set of gene products for GO term enrichment
|
2025-03-25 |
|
perl-text-template-simple
|
public |
Simple text template engine
|
2025-03-25 |
|
matlock
|
public |
Simple tools for working with Hi-C data
|
2025-03-25 |
|
scaffold_builder
|
public |
Scaffold_builder: Combining de novo and reference-guided assembly with Scaffold_builder.
|
2025-03-25 |
|
perl-bio-rna-rnaalisplit
|
public |
Split and deconvolute structural RNA multiple sequence alignments
|
2025-03-25 |
|
perl-array-set
|
public |
Perform set operations on arrays
|
2025-03-25 |
|
enabrowsertools
|
public |
enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily
|
2025-03-25 |
|
anise_basil
|
public |
BASIL is a method to detect breakpoints for structural variants (including insertion breakpoints) from aligned paired HTS reads in BAM format. ANISE is a method for the assembly of large insertions from paired reads in BAM format and a list candidate insert breakpoints as generated by BASIL.
|
2025-03-25 |
|
bcool
|
public |
BCOOL is a read corrector for NGS sequencing data that align reads on a de Bruijn graph. Version described at (https://arxiv.org/abs/1711.03336) presented at RECOMB-seq 2018
|
2025-03-25 |
|
fastsimbac
|
public |
Models bacterial recombination
|
2025-03-25 |
|
cromshell
|
public |
Command-line interface to the Cromwell workflow manager
|
2025-03-25 |
|
cnv_facets
|
public |
Detect somatic copy number variants (CNV) in tumour-normal samples using next generation sequencing data
|
2025-03-25 |
|
hmftools-amber
|
public |
Generates a tumor BAF file for use in PURPLE.
|
2025-03-25 |
|
bioconductor-decontam
|
public |
Identify Contaminants in Marker-gene and Metagenomics Sequencing Data
|
2025-03-25 |
|
biothings_client
|
public |
Python Client for BioThings API services.
|
2025-03-25 |
|
xmatchview
|
public |
Genome sequence alignment visualization
|
2025-03-25 |
|
lambda
|
public |
Lambda is a local aligner optimized for many query sequences and searches in protein space
|
2025-03-25 |
|
dropletutils-scripts
|
public |
CLI scripts for the DropletUtils package
|
2025-03-25 |
|
snp-pileup
|
public |
Compute SNP pileup at reference positions in one or more input bam files. Output is ready for the R package facets
|
2025-03-25 |
