bioconda / packages

Package Name Access Summary Updated
digestiflow-cli public Command line client for Digestiflow. 2019-04-18
perl-moosex-app public Write user-friendly command line apps with even less suffering 2019-04-18
hyphy public HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning. 2019-04-18
tango public Assign taxonomy to metagenomic contigs 2019-04-18
r-stitch public STITCH - Sequencing To Imputation Through Constructing Haplotypes 2019-04-18
bioconductor-dupradar public Duplication rate quality control for RNA-Seq datasets. 2019-04-17
perl-html-parser public HTML parser class 2019-04-17
perl-pathtools public Tools for working with directory and file names 2019-04-17
mark-nonconverted-reads public A simple filter to mark potential nonconverted reads from methylation experiments 2019-04-17
parallel-fastq-dump public parallel fastq-dump wrapper 2019-04-17
nextflow public A DSL for data-driven computational pipelines http://nextflow.io 2019-04-17
bismark public Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. 2019-04-17
fastp public A FASTQ preprocessor with full features (QC/adapters/trimming/filtering/splitting...) 2019-04-17
pathogist public Calibrated multi-criterion genomic analysis for public health microbiology 2019-04-17
fwdpy11 public Forward-time population genetic simulation in Python. 2019-04-17
r-seurat public A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details. 2019-04-16
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
deepac public Predicting pathogenic potentials of novel DNA with reverse-complement neural networks. 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
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