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bioconductor-rsubread
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public |
Mapping, quantification and variant analysis of sequencing data
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2025-04-22 |
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mofapy
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public |
Multi-Omics Factor Analysis
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2025-04-22 |
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graphaligner
|
public |
Sequence to graph aligner for long reads
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2025-04-22 |
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kwip
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public |
kWIP implements a de novo, alignment free measure of sample genetic dissimilarity
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2025-04-22 |
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r-stitch
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public |
STITCH - Sequencing To Imputation Through Constructing Haplotypes.
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2025-04-22 |
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r-cellassign
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public |
Automated, probabilistic assignment of cell types in scRNA-seq data
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2025-04-22 |
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r-pophelper
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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.
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2025-04-22 |
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unifrac
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public |
Fast phylogenetic diversity calculations
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2025-04-22 |
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readfq
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public |
A high-speed tool to calculate reads number and total base count in FASTQ file, forked from Li Heng's original version
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2025-04-22 |
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consel
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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
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2025-04-22 |
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picrust2
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public |
PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States
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2025-04-22 |
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islandpath
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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.
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2025-04-22 |
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perl-moosex-singleton
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public |
Turn your Moose class into a singleton
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2025-04-22 |
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gappa
|
public |
Genesis Applications for Phylogenetic Placement Analysis
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2025-04-22 |
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ir
|
public |
Program for Calculating the Repetitiveness of DNA Sequences
|
2025-04-22 |
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digestiflow-demux
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public |
Digestiflow Command Line Client.
|
2025-04-22 |
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digestiflow-cli
|
public |
Command line client for Digestiflow.
|
2025-04-22 |
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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.
|
2025-04-22 |
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xpclr
|
public |
Code to compute xp-clr values to detect selection as per Chen, Patterson & Reich 2010.
|
2025-04-22 |
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perl-local-lib
|
public |
create and use a local lib/ for perl modules with PERL5LIB
|
2025-04-22 |
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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.
|
2025-04-22 |
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calour
|
public |
exploratory and interactive microbiome analyses based on heatmaps
|
2025-04-22 |
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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.
|
2025-04-22 |
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faststructure
|
public |
A variational framework for inferring population structure from SNP genotype data.
|
2025-04-22 |
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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.
|
2025-04-22 |
