bioconda / packages

Package Name Access Summary Updated
amas public Calculate various summary statistics on a multiple sequence alignment 2019-04-16
damageprofiler public A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage 2019-04-16
varfish-annotator-cli public Annotate variants for import into VarFish Server. 2019-04-16
snp-pileup public Compute SNP pileup at reference positions in one or more input bam files. Output is ready for the R package facets 2019-04-16
openmg public Exhaustive generation of chemical structures 2019-04-16
rmats public MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. 2019-04-16
gffcompare public GffCompare by Geo Pertea 2019-04-16
pathwaymatcher public PathwayMatcher is a software tool writen in Java to search for pathways related to a list of proteins in Reactome. 2019-04-16
stamp public A graphical software package for analyzing taxonomic and functional profiles. 2019-04-15
transit public TRANSIT 2019-04-15
medaka public Neural network sequence error correction. 2019-04-15
multiqc public Create aggregate bioinformatics analysis reports across many samples and tools 2019-04-15
gxformat2 public Galaxy Workflow Format 2 Descriptions 2019-04-14
scprep public Tools for loading and preprocessing biological matrices in Python. 2019-04-14
galaxy-lib public Subset of Galaxy (http://galaxyproject.org/) core code base designed to be used a library. 2019-04-14
sciphi public Single-cell mutation identification via phylogenetic inference 2019-04-14
probcons public PROBCONS is a probabilistic consistency-based multiple sequence alignment 2019-04-14
bcbio-nextgen public Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis 2019-04-13
methyldackel public A (mostly) universal methylation extractor for BS-seq experiments. Formerly named PileOMeth. 2019-04-13
braker2 public BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction. 2019-04-13
augustus public AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments. 2019-04-13
graphaligner public Sequence to graph aligner for long reads 2019-04-13
mapping-iterative-assembler public Consensus calling or `reference assisted assembly`, chiefly of ancient mitochondria. 2019-04-12
tb-profiler public Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data 2019-04-12
snakemake public Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files. This package provides the full installation including all optional dependencies. 2019-04-12
snakemake-minimal public Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files. This package provides the core snakemake functionility. For features like reports and remote files, check out the snakemake package which provides all optional dependencies. 2019-04-12
pairix public 2D indexing on bgzipped text files of paired genomic coordinates 2019-04-12
cytoscape public Cytoscape: an open source platform for network analysis and visualization. 2019-04-12
bioblend public CloudMan and Galaxy API library 2019-04-12
pathogen-profiler public Library giving access to classes and functions to create a profiling tool to look for mutations from NGS data. 2019-04-12
deepvariant public DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data 2019-04-12
ipython-cluster-helper public Tool to easily start up an IPython cluster on different schedulers 2019-04-12
bcbio-nextgen-vm public Run bcbio-nextgen genomic sequencing analyses using isolated containers and virtual machines 2019-04-12
jannovar-cli public Java tool for performing annotation of VCF files 2019-04-12
spaln public Map and align a set of cDNA/EST or protein sequences onto a genome 2019-04-12
collect-columns public Retrieve a column for each in a set of tables, placing them in a single output table. 2019-04-12
fgbio public A set of tools for working with genomic and high throughput sequencing data, including UMIs 2019-04-12
onto2nx public A package for parsing ontologies in the OWL and OBO format into NetworkX graphs 2019-04-12
biobb_model public Biobb_model is the Biobb module collection to check and model 3d structures, create mutations or reconstruct missing atoms. 2019-04-11
bioconductor-mapkl public We proposie a hybrid FS method (mAP-KL), which combines multiple hypothesis testing and affinity propagation (AP)-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes. 2019-04-11
biobb_analysis public Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations. 2019-04-11
snp-mutator public Generate mutated sequence files from a reference genome. 2019-04-11
biobb_common public Biobb_common is the base package required to use the biobb packages. 2019-04-11
crispr_studio public CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization 2019-04-11
rust-bio-tools public A growing collection of fast and secure command line utililities for dealing with NGS data implemented on top of Rust-Bio. 2019-04-11
jbrowse public The JBrowse Genome Browser 2019-04-11
dendropy public A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. 2019-04-11
micall-lite public A bioinformatic pipeline for mapping FASTQ data to a set of reference sequences to generate consensus sequences, variant calls and coverage maps. 2019-04-10
segtools public a python package for analyzing genomic segmentations 2019-04-10
nanoplot public Plotting suite for long read sequencing data and alignments 2019-04-10
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