bioconda / packages

Package Name Access Summary Updated
ascat public ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy (Figure 1). ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell, expressed as multiples of haploid genomes) from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome). 2023-03-28
snakemake-wrapper-utils public A collection of utility functions and classes for Snakemake wrappers. 2023-03-28
imods public toolkit to perform Normal Mode Analysis (NMA) in internal coordinates (IC) on both protein and nucleic acid atomic structures. 2023-03-28
oakvar public OakVar - Genomic Variant Analysis Platform 2023-03-28
r-recetox-aplcms public apLCMS is a software which generates a feature table from a batch of LC/MS spectra. A modified fork of the original apLCMS by Tianwei Yu. 2023-03-27
flye public Fast and accurate de novo assembler for single molecule sequencing reads 2023-03-27
endorspy public calculates endogenous DNA from samtools flagstat files and print to screen 2023-03-27
bioconda-repodata-patches public generate tweaks to index metadata, hosted separately from index 2023-03-27
fwdpy11 public Forward-time population genetic simulation in Python. 2023-03-26
quatradis public A set of tools to analyse the output from TraDIS analyses 2023-03-25
hmftools-sv-prep public SV Prep generates a maximally filtered SV BAM file by identifying candidate SV junctions and extracting all reads that may provide support to that junction. 2023-03-25
grampa public GRAMPA is a program to identify and place polyploidy events on a phylogeny and to count duplications and losses in the presence of polyploidy. 2023-03-25
pymsaviz public MSA visualization python package for sequence analysis 2023-03-25
dxpy public DNAnexus Platform API bindings for Python 2023-03-25
bioconda-utils public Utilities for building and managing bioconda recipes. 2023-03-25
efishent public A tool to design RNA FISH oligos/probes 2023-03-24
ngsderive public Backwards derive attributes from NGS data 2023-03-24
foldcomp public Foldcomp: a library and format for compressing and indexing large protein structure sets 2023-03-24
shigeifinder public Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies 2023-03-24
ganon public ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently 2023-03-24
svjedi-graph public SVJedi-graph is a structural variation (SV) genotyper for long read data using a variation graph to represent SVs. 2023-03-24
read2tree public Building phylogenetic trees directly from sequencing reads 2023-03-23
bioconductor-dexseq public Inference of differential exon usage in RNA-Seq 2023-03-23
hifiasm public Haplotype-resolved assembler for accurate Hifi reads 2023-03-23
dragonflye public Microbial assembly pipeline for Nanopore reads 2023-03-23
mafft public Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform 2023-03-23
r-shinyngs public Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion. 2023-03-23
snakemake public A popular workflow management system aiming at full in-silico reproducibility. 2023-03-23
snakemake-minimal public A popular workflow management system aiming at full in-silico reproducibility. 2023-03-23
proteinortho public Proteinortho is a tool to detect orthologous genes within different species. 2023-03-23
marvd2 public Metagenomic Archaeal Virus Detector 2 2023-03-23
riassigner public GC-MS retention index calculation 2023-03-23
kseqpp public C++11 re-implementation of kseq by Heng Li 2023-03-23
vibrant public Virus Identification By iteRative ANnoTation 2023-03-23
rnabloom public Java tool for RNA-seq assembly 2023-03-23
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. 2023-03-23
segmetrics public A Python package implementing image segmentation and object detection performance measures, for biomedical image analysis and beyond. 2023-03-23
gtdbtk public A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. 2023-03-23
haptools public Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis 2023-03-23
fiji-simple_omero_client public Java library to simplify API to put/get objects on an OMERO server from Fiji/ImageJ. 2023-03-22
gtotree public GToTree is a user-friendly workflow for phylogenomics. 2023-03-22
querynator public Python package to query cancer variant databases 2023-03-22
alignoth public A tool for creating alignment plots from bam files 2023-03-22
seqscreen public SeqScreen was created to sensitively assign taxonomic classifications, functional annotations, and Functions of Sequences of Concern (FunSoCs) to single, short DNA sequences or open reading frames. 2023-03-22
svhip public Retrainable machine learning pipeline for the detection of secondary structure conservation on a genome-level. 2023-03-22
xs-sim public Simulates NGS reads 2023-03-22
guidemaker public GuideMaker: Software to design gRNAs pools in non-model genomes and CRISPR-Cas systems 2023-03-22
micom public Microbial community modeling based on cobrapy. 2023-03-22
cellqc public Cellqc standardizes the qualiy control of single-cell RNA-Seq (scRNA) data to render clean feature count matrices. 2023-03-22
savana public SAVANA: a somatic structural variant caller for long-read data 2023-03-22

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