bioconda

There are 3 repositories under bioconda topic.

MultiQC / MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
bioinformatics analysis pypi bioconda multiqc python data-visualization quality-control reporting seqera vizualisation
Language:JavaScript 1178
fritzsedlazeck / Sniffles
Structural variation caller using third generation sequencing
bioinformatics structural-variations ngm-lr pacbio nanopore structural-variation bioconda
Language:Python 515
genomepy
vanheeringen-lab / genomepy
genes and genomes at your fingertips
genome bioconda python ensembl ucsc ncbi
Language:Python 363
bactopia
bactopia / bactopia
A flexible pipeline for complete analysis of bacterial genomes
bacterial-genomes nextflow fastqs conda bioconda
Language:Nextflow 360
fritzsedlazeck / SURVIVOR
Toolset for SV simulation, comparison and filtering
bioinformatics structural-variations simulator comparison survivor vcf bioconda
Language:C++ 330
philres / ngmlr
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
next-generation-sequencing pacbio oxford-nanopore mapper structural-variations long-read alignment bioconda docker
Language:C++ 284
bioinfo-notebook
rnnh / bioinfo-notebook
🔬 Bioinformatics Notebook. Scripts for bioinformatics pipelines, with quick start guides for programs and video demonstrations.
bioinformatics bash bash-script conda bioconda bioinformatics-programs bioinformatics-notebook featurecounts ubuntu fastq-dump windows-subsystem video-demonstration
Language:Shell 144
linnabrown / run_dbcan
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
dbcan database webserver docker bioinformatics anaconda bioconda
Language:Python 128
althonos / pyrodigal
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
orf-finder metagenomes python bioconda python-library cython-wrapper python-interface prodigal genome gene-finding bioinformatics simd
Language:Cython 122
seqfu2
telatin / seqfu2
:rocket: seqfu - Sequece Fastx Utilities
fastq fasta bioinformatics bioinformatics-tool bioconda genomics ngs sequencing
Language:Nim 102
urmi-21 / pyrpipe
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
rna-seq rna-seq-pipeline ncbi-sra bioinformatics bioinformatics-pipeline bioinformatics-analysis python rna-seq-workflows conda bioconda
Language:Python 77
Clinical-Genomics / chanjo
Chanjo provides a better way to analyze coverage data in clinical sequencing.
bioconda coverage sambamba python sql genomics
Language:Python 48
telatin / covtobed
⛰ covtobed | Convert the coverage track from a BAM file into a BED file
bioinformatics bioinformatics-tool bioconda bed alignments bam-files sequence-coverage
Language:C++ 44
cmkobel / assemblycomparator2
🦠📇 Compare prokaryotic genomic assemblies
microbial-genomics snakemake genomes-to-report hpc conda apptainer bioinformatics pbs slurm bioconda prokaryotes metagenomics clinical-research
Language:Python 23
ypriverol / containers-rules-manuscript
Recommendations to contenarized your bioinformatics software
biocontainers docker rkt conda bioconda
Language:Shell 11
mpc-bioinformatics / ProtGraph
ProtGraph - A Graph-Generator for Proteins
graph peptide fasta protein python3 pypi bioconda uniprot
Language:Python 9
burkesquires / Build-a-Reproducible-Jupyter-Workflow-From-Scratch
Build a Reproducible Jupyter Workflow From Scratch (2017 NIH Hour of Code)
hour-of-code jupyter-notebook jupyter python python3 anaconda-distribution bioconda bioinformatics nih niaid workflow
Language:Jupyter Notebook 8
BioContainers / edu
BioContainers Documentation.
documentation-code travis documentation readthedocs containers biocontainers bioconda
Language:JavaScript 7
MonashBioinformaticsPlatform / bioconda-tutorial
A quick overview of how to use Bioconda, and create recipes
bioconda bioinformatics tutorial
Language:Jupyter Notebook 6
gifford-lab / deepaccess-package
Methods for training and interpretation of an ensemble of neural networks for multi-task functional prediction of accessibility or histone modifications from DNA sequence.
deep-learning interpretation genomics epigenomics bioconda pypi-package
Language:Python 5
Quansight-Labs / czi-conda-forge-mgmt
🚀 Top level project management for conda-forge CZI grant
bioconda conda-forge
5
telatin / qax
Qiime2 Artifact eXtractor
qiime2 qiime2-installation metadata metabarcoding artifacts qax bioinformatics bioinfo bioconda
Language:Nim 5
bioconda / bioconda-paper
Data analysis related to the bioconda paper
analysis-workflows bioconda reproducibility snakemake
Language:Python 4
NordicESMhub / containers
Containers for running ESM related tools
climate containers bioconda esm docker-container cesm hacktoberfest
Language:SCSS 4
asadprodhan / A-beginner-s-guide-to-Bioinformatics
A beginner’s guide to Bioinformatics
bash bedtools bioconda bioinformatics blastn conda conda-environment
3
bioconda / bioconda-plots
Generating various plots for the bioconda homepage
bioconda plot
Language:Python 3
jlanga / exfi
Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools
transcriptomics rna-seq assembly kmer bloom-filter abyss bedtools python3 conda bioconda biobloomtools exon transcriptome abyss-bloom biopython pandas network splice-graphs
Language:Python 3
mv-lab / dna-proto-workflow
Snakemake ProtoWorkflow for DNA Analysis.
snakemake dna bioconda
Language:Python 3
dfloresDIL / MEGA
MEGA ATAC-seq Workflow implementation
atac-seq snakemake conda bioconda ngs-pipeline
Language:Python 2
sk-sahu / PGRB
Practical Guide to Reproducibility in Bioinformatics (Work In Progress)
reproducibility bioinformatics reproducible-science reproducible-analysis reproducible-research workflow-automation jupyter-notebook rmarkdown docker biocontainers conda conda-environment bioconda domain-specific-language
Language:Nextflow 2
fatmakahveci / milestone
bacterial strain identification
graph bacteria python snakemake strain bacterial-strain bacterial-genomes bioconda bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-scripts bioinformatics-tool conda snakemake-pipeline snakemake-workflow
Language:Python 1
Genometric / TVQ
Contains scripts to study the impact of publishing software to package management systems on their scholarly recognition.
scholarly-references biotools bioconductor bioconda toolshed citation
Language:C# 1
lauralwd / Azolla_genus_metagenome
This project aims do describe and explore the metagenomes of fern species of the genus Azolla.
azolla symbiosis metagenomes plant metagenomics metagenomic-pipeline metagenome-assembly snakemake conda bioconda bioinformatics bioinformatics-pipeline biological-data-analysis fair-data endophytes symbiont
Language:Python 1
lucianhu / Bash-script-DNA-Sequence
Linux command-line to analyse next-generation sequencing (NGS) data
bioconda bioinformatics linux miniconda ngs-analysis ngs-pipeline
1
bio-TAGI / Hackathon
Analysis of mutations at codon 625 of SF3B1 gene in uveal melanoma
rna-seq-pipeline workflow bioinformatics analysis computational-biology nextflow python r conda docker bioconda
Language:R 0
jhammelman / deepaccess-package
Training an interpretation of ensemble of convolutional neural networks for multi-task functional genomic classification tasks.
deep-learning genomics epigenomics bioconda
Language:Python 0