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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).
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2023-03-28 |
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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 |
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oakvar
|
public |
OakVar - Genomic Variant Analysis Platform
|
2023-03-28 |
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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 |
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flye
|
public |
Fast and accurate de novo assembler for single molecule sequencing reads
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2023-03-27 |
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endorspy
|
public |
endorS.py calculates endogenous DNA from samtools flagstat files and print to screen
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2023-03-27 |
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bioconda-repodata-patches
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public |
generate tweaks to index metadata, hosted separately from anaconda.org index
|
2023-03-27 |
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fwdpy11
|
public |
Forward-time population genetic simulation in Python.
|
2023-03-26 |
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quatradis
|
public |
A set of tools to analyse the output from TraDIS analyses
|
2023-03-25 |
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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 |
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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.
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2023-03-25 |
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pymsaviz
|
public |
MSA visualization python package for sequence analysis
|
2023-03-25 |
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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 |