Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

Package Usage: conda: pymdown-extensions

PyMdown Extensions is a collection of extensions for Python Markdown. They were originally written to make writing documentation more enjoyable. They cover a wide range of solutions, and while not every extension is needed by all people, there is usually at least one useful extension for everybody.
1 version
Latest release: about 1 year ago
1 dependent package

View more package details: https://packages.ecosyste.ms/registries/anaconda.org/packages/pymdown-extensions

View more repository details: https://repos.ecosyste.ms/hosts/GitHub/repositories/facelessuser%2Fpymdown-extensions

Dependent Repos 70

GCJMackenzie/sarek Fork of nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  • 6.0 environment.yml

Size: 16.4 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

bsbtd/Teste
  • 6.0.* proteomicslfq/environment.yml

Size: 535 MB - Last synced: 17 days ago - Pushed: 17 days ago

openproblems-bio/nf-openproblems
  • 6.0.* environment.yml

Size: 197 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

oeg-upm/TPDL2022_FAIROs
  • 7.1.* experiment1/research_object/environment.yml

Size: 85.9 KB - Last synced: 10 months ago - Pushed: almost 2 years ago

nicni16/nfcore-maxquant
  • 8.1.1.* environment.yml

Size: 48.8 MB - Last synced: 9 months ago - Pushed: about 3 years ago

SystemsGenetics/GEMmaker
A workflow for construction of Gene Expression count Matrices (GEMs). Useful for Differential Gene Expression (DGE) analysis and Gene Co-Expression Network (GCN) construction
  • 8.1.1.* environment.yml

Size: 12.8 MB - Last synced: about 2 months ago - Pushed: 4 months ago

lauramble/rnaseq-vizfada
  • 6.0.* environment.yml

Size: 5.63 MB - Last synced: 14 days ago - Pushed: almost 2 years ago

GuilleGorines/nfcore-pikavirus-legacy 📦
  • 7.1.* environment.yml

Size: 348 KB - Last synced: about 1 year ago - Pushed: about 3 years ago

lifebit-ai/gel-gwas-nf
  • 6.0.* environment.yml

Size: 3.49 MB - Last synced: about 1 month ago - Pushed: over 2 years ago

lifebit-ai/relate
Genomics Englands' Ancestry and Relatedness inference workflow
  • 6.0.* environment.yml

Size: 718 KB - Last synced: about 1 month ago - Pushed: about 1 year ago

lifebit-ai/siteqc
Genomics England's workflow for variant annotation and quality control.
  • 6.0.* environment.yml

Size: 242 KB - Last synced: about 1 month ago - Pushed: over 3 years ago

nibscbioinformatics/scoop
Another metagenomics pipeline with a cookery name. The pipeline is based on read classification (i.e. no assembly) and uses biobakery tools.
  • 6.0.* environment.yml

Size: 240 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

nibscbioinformatics/scranger
scRNAseq Pipeline running Cell Ranger and Seurat
  • 6.0.* environment.yml

Size: 237 KB - Last synced: 7 months ago - Pushed: over 3 years ago

nibscbioinformatics/viralevo
  • 6.0.* environment.yml

Size: 308 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

lifebit-ai/annotate
  • 6.0.* environment.yml

Size: 164 KB - Last synced: about 1 month ago - Pushed: over 3 years ago

steffenlem/sradownloader
A pipeline to download raw data from SRA
  • 6.0.* environment.yml

Size: 209 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

nibscbioinformatics/nanoprofiler
Profiling Nanobodies sequencing libraries
  • 6.0.* environment.yml

Size: 2.43 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

genomicsITER/NanoCLUST
NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
  • 8.0.* conda_envs/output_documentation/environment.yml

Size: 6.7 MB - Last synced: 4 months ago - Pushed: 6 months ago

med-team/nf-core-artic
nf-core ARTIC field bioinformatics viral genome pipeline
  • 6.0.* environment.yml

Last synced: over 1 year ago

edotau/fishingcluster
  • 6.0.* workflows/rnaseq/environment.yml

Size: 3.74 MB - Last synced: about 1 year ago - Pushed: about 3 years ago

yocra3/Episignatures
Generate episignatures for different diseases
  • docker_sources/python_session/environment.yml

Size: 1.37 MB - Last synced: 4 months ago - Pushed: 10 months ago

bioinfo-pf-curie/ATAC-seq
Nextflow pipeline for ATAC-seq data analysis
  • 7.1 environment.yml

Size: 3.41 MB - Last synced: 5 months ago - Pushed: over 1 year ago

BU-ISCIII/assemblybacterias Fork of luissian/assemblybacterias_pipeline
  • 6.0.* environment.yml

Size: 3.82 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

lifebit-ai/phewas
Performs a PheWAS analysis & generates a Manhattan plot using the PheWAS R package
  • 6.0.* environment.yml

Size: 6.78 MB - Last synced: about 1 month ago - Pushed: about 1 year ago

lifebit-ai/gwas
GWAS pipeline using SAIGE
  • 6.0.* environment.yml

Size: 37.4 MB - Last synced: about 1 month ago - Pushed: about 1 year ago

chelauk/nf-core-umi_preprocessing
  • 6.0.* environment.yml

Size: 2.57 MB - Last synced: 9 months ago - Pushed: about 2 years ago

AndreaMariani-AM/Docker
This repo contains github actions to build various Docker Images
  • 7.1.* HiC-snakemake/environment.yml

Size: 322 KB - Last synced: 10 months ago - Pushed: 10 months ago

lifebit-ai/nf-rnaseq-salmon
  • 6.0.* environment.yml

Size: 69.9 MB - Last synced: about 1 month ago - Pushed: about 1 year ago

aalinebini/ampliconseq
  • 6.0.* environment.yml

Size: 152 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago

FAANG/GSM-pipeline
  • 8.1.1.* environment.yml

Size: 18.8 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

subwaystation/pangenome Fork of nf-core/pangenome
  • 7.1.* environment.yml

Size: 3.88 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

AI4EPS/homepage
AI4EPS: Artificial Intelligence for Earth and Planetary Science
  • 9.9.1 .github/environment.yml

Size: 106 MB - Last synced: 24 days ago - Pushed: 24 days ago

hitszosa/wiki
Repository of HITSZ OSA Wiki
  • 9.5 environment.yml

Size: 329 KB - Last synced: 15 days ago - Pushed: 16 days ago

rtourdot/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  • 6.0 environment.yml

Last synced: over 1 year ago

qbic-pipelines/cellranger
Nextflow pipeline wrapper for executing Cell Ranger
  • 6.0.* environment.yml

Size: 23.4 MB - Last synced: 7 months ago - Pushed: about 2 years ago

rvntwiki/wiki
A personal wiki
  • 9.1 docs/environment.yaml
  • 8.1.1 site/environment.yaml

Last synced: 12 months ago

ablab/metaGT
Pipeline for metagenome and metatranscriptome joint assembly
  • 8.2.* environment.yml

Size: 1.96 MB - Last synced: about 2 hours ago - Pushed: about 1 year ago

LBEG_INTA/NanoCLUST
NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
  • 8.0.* conda_envs/output_documentation/environment.yml

Last synced: over 1 year ago

AI4EPS/QuakeFlow
QuakeFlow: A Scalable Deep-learning-based Earthquake Monitoring Workflow with Cloud Computing
  • 9.9.1 .github/environment.yml

Size: 17 MB - Last synced: 24 days ago - Pushed: 24 days ago

GuilleGorines/BU_ISCIII-bacterial-assembly Fork of BU-ISCIII/assemblybacterias
  • 6.0.* environment.yml

Size: 3.74 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

t-neumann/slamseq
nf-core slamseq development repository
  • 6.0.* environment.yml

Size: 2 MB - Last synced: 7 months ago - Pushed: over 3 years ago

lauramarie99/nf_methylseq_prak Fork of nf-core/methylseq
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  • 8.1.1.* environment.yml

Size: 18.7 MB - Last synced: about 1 month ago - Pushed: over 1 year ago

NextRNAtx/clipseq Fork of nf-core/clipseq
CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.
  • 6.0.* environment.yml

Size: 39.2 MB - Last synced: 10 months ago - Pushed: over 1 year ago

ICESAT-2HackWeek/website2022
ICESat-2 Hackweek 2022 landing page and jupyter book
  • 9.2 binder/environment.yml
  • >=7.1 conda/environment.yml

Size: 69.6 MB - Last synced: about 1 month ago - Pushed: over 1 year ago

sheynkman-lab/Long-Read-Proteogenomics
A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.
  • 6.0.* environment.yml

Size: 108 MB - Last synced: 7 months ago - Pushed: over 1 year ago

sheffield-bioinformatics-core/NanoCLUST Fork of genomicsITER/NanoCLUST
NanoCLUST is an analysis pipeline for UMAP-based classification of amplicon-based full-length 16S rRNA nanopore reads
  • 8.0.* conda_envs/output_documentation/environment.yml

Size: 6.88 MB - Last synced: 5 months ago - Pushed: 5 months ago

AI4EPS/DeepDenoiser
DeepDenoiser: Seismic Signal Denoising and Decomposition Using Deep Neural Networks
  • 9.9.1 .github/environment.yml

Size: 33.5 MB - Last synced: 7 months ago - Pushed: 7 months ago

NASA-Openscapes/edlfs
POC to test access patterns to NASA datasets.
  • 9.2.* environment.yml

Size: 328 KB - Last synced: about 1 month ago - Pushed: about 1 year ago

ericmjl/Network-Analysis-Made-Simple
An introduction to network analysis and applied graph theory using Python and NetworkX
  • environment.yml

Size: 299 MB - Last synced: 1 day ago - Pushed: 1 day ago

heuermh/artic
UNDER CONSTRUCTION: nf-core ARTIC field bioinformatics pipeline
  • 6.0.* environment.yml

Size: 205 KB - Last synced: 20 days ago - Pushed: about 4 years ago

suzannejin/nf-proportionality
  • 6.0.* environment.yml

Size: 167 MB - Last synced: about 1 year ago - Pushed: about 3 years ago

ameynert/ega-submission-via-portal
  • 6.0.* environment.yml

Size: 11.4 MB - Last synced: about 21 hours ago - Pushed: over 2 years ago

biocompute-objects/bco-ro-example-chipseq
Packaging a IEEE 2791 described BioCompute Object as RO-Crate, using nf-core/chipseq as example
  • 7.1.* data/environment.yml

Size: 107 MB - Last synced: about 1 month ago - Pushed: about 3 years ago

Shicheng-Guo/gwasgsa
Gene-set Analysis for GWAS studies using MAGMA
  • 6.0.* environment.yml

Size: 189 KB - Last synced: 7 months ago - Pushed: almost 3 years ago

veitveit/nf-core-wombatp
  • 6.0.* environment.yml

Size: 98.6 KB - Last synced: 9 months ago - Pushed: almost 3 years ago

lescailab/binder_biopython
Biopython teaching using binder technologies
  • environment.yml

Size: 9.77 KB - Last synced: about 1 year ago - Pushed: about 3 years ago

oronoc1210/MA5112-Genomics_Data_Analysis_II
Nextflow script and environment created for the final project of NUIG's MA5112: Genomics Data Analysis II course. Project was to develop a CLIP-seq pipeline using nextflow. The project was conducted in a group with Claire Coleman, Clare Lamont, Aine Halpin, and Oisin McCaffrey.
  • 6.0.* environment.yml

Size: 5.86 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago

Genomic-Medicine-Linkoping/nf-core-sarek
  • 6.0 environment.yml

Size: 6.25 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago

lescailab/toolprofiler
  • 6.0.* environment.yml

Size: 141 KB - Last synced: about 1 year ago - Pushed: about 3 years ago

Simontuk/sprint_covseq
Covseq-pipe nextflow
  • 7.1.* environment.yml

Size: 1.59 MB - Last synced: about 1 year ago - Pushed: about 3 years ago

jsimonas/solo-in-drops
STARsolo wrapper for inDrops analysis
  • 6.0.* environment.yml

Size: 324 KB - Last synced: 7 months ago - Pushed: 9 months ago

kalenkovich/reproducible-data-analysis
Исходники материалов к занятиям по репродуцируемому анализу данных на летней школе Елены Горбуновой в 2020 году.
  • 8.0.1.* environment.yml

Size: 5.68 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

FriederikeHanssen/shrnacount
  • 6.0.* environment.yml

Size: 75.2 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

FriederikeHanssen/babysarek
  • 6.0.* environment.yml

Size: 209 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

lengfei5/nf_visium_kallisto
  • 7.1.* environment.yml

Size: 2.12 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

Scott-Hickmann/Article-Rewriter
  • environment.yml

Size: 1.13 MB - Last synced: 10 months ago - Pushed: about 1 year ago

jtmccr1/nf-core-phylofunk
An nf-core compatible pipeline for running BEAST analysis
  • 6.0.* environment.yml

Size: 1.97 MB - Last synced: 9 months ago - Pushed: almost 3 years ago

keng404/nextflow_test
cwl-wrapped nextflow pipeline for ICA (Illumina Connected Analytics)
  • 6.0.* environment.yml
  • 6.0.* hlatyping/environment.yml

Size: 13.1 MB - Last synced: 8 months ago - Pushed: 8 months ago

steffenlem/querysra
This pipeline queries the SRA database using metadata information
  • 7.1.* environment.yml

Size: 111 KB - Last synced: about 1 year ago - Pushed: about 4 years ago

lengfei5/nf_atacseq
  • 7.1.* environment.yml

Size: 1.29 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

bhagesh-codebeast/nextflowdualrnaseq
  • 6.0.* environment.yml

Size: 35.7 MB - Last synced: about 1 year ago - Pushed: about 3 years ago

sripaladugu/germline_somatic
  • 6.0 environment.yml

Size: 5.09 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

SystemsGenetics/transcript_corral
  • 8.1.1.* environment.yml

Size: 543 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

bioinfo-pf-curie/vegan
Variant calling pipeline for whole Exome and whole Genome sequencing cANcer data
  • 8.1.1.* recipes/conda/environment.yml

Size: 0 Bytes - Last synced: about 1 year ago - Pushed: over 2 years ago

bioinfo-pf-curie/as-mapping
Nextflow pipeline for Allele-specific analysis
  • 7.1.* environment.yml

Size: 336 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

jpfeuffer/proteomicsTMT
nf-core pipeline for proteomics TMT analysis
  • 8.0.1.* environment.yml

Size: 25.5 MB - Last synced: 10 months ago - Pushed: over 2 years ago

Collinbrown95/prototype-diagrams-docs-site
A prototype mkdocs documentation site for the mingrammer/diagrams project: https://github.com/mingrammer/diagrams
  • 9.5.* environment.yml

Size: 521 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago

GenomicsNX/NGI-ChIPseq Fork of nf-core/chipseq
Nextflow ChIP-seq data analysis pipeline, National Genomics Infrastructure, Science for Life Laboratory in Stockholm
  • 7.1.* environment.yml

Size: 11.3 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago

JoBBurt/proteomicslfq Fork of nf-core/proteomicslfq
Proteomics label-free quantification (LFQ) analysis pipeline
  • 8.0.1.* environment.yml

Size: 886 KB - Last synced: 10 months ago - Pushed: over 3 years ago

ncarrut/proteomicslfq Fork of nf-core/proteomicslfq
Proteomics label-free quantification (LFQ) analysis pipeline
  • 8.0.1.* environment.yml

Size: 850 KB - Last synced: 10 months ago - Pushed: over 3 years ago

cguyomar/smrnaseq Fork of nf-core/smrnaseq
A small-RNA sequencing analysis pipeline
  • 6.0.* environment.yml

Size: 6.59 MB - Last synced: 10 months ago - Pushed: almost 3 years ago

cguyomar/sarek Fork of nf-core/sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  • 6.0 environment.yml

Size: 11.9 MB - Last synced: 10 months ago - Pushed: about 2 years ago

jamontanac/Network-Analysis-Made-Simple Fork of ericmjl/Network-Analysis-Made-Simple
An introduction to network analysis and applied graph theory using Python and NetworkX
  • environment.yml

Size: 294 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago

BharatPanera/chipseq Fork of nf-core/chipseq
ChIP-seq peak-calling, QC and differential analysis pipeline.
  • 7.1.* environment.yml

Size: 14.4 MB - Last synced: 10 months ago - Pushed: almost 2 years ago

wkljohn/smartseq2 Fork of nf-core/smartseq2 📦
A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.
  • 6.0.* environment.yml

Size: 2.59 MB - Last synced: 10 months ago - Pushed: over 2 years ago

jsimonas/drop-srna-seq
drop-srna-seq
  • 6.0.* environment.yml

Size: 160 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

lqsae/hlatyping Fork of nf-core/hlatyping
Precision HLA typing from next-generation sequencing data
  • 6.0.* environment.yml

Size: 38.9 MB - Last synced: about 1 month ago - Pushed: almost 3 years ago

zachghiaccio/ICESat-2-Hackweek-2023 Fork of fliphilipp/ICESat-2-Hackweek-2023
ICESat-2 Hackweek 2023 tutorials and event website
  • 9.5 binder/environment.yml
  • >=7.1 conda/environment.yml

Size: 172 MB - Last synced: 10 months ago - Pushed: 10 months ago

akshaips/nf-core-metabolinden Fork of PayamEmami/nf-core-metabolinden
Metabolomics quaLIty coNtrol anD paramEter optimizatioN
  • 8.0.1.* environment.yml

Size: 2.04 MB - Last synced: 10 months ago - Pushed: over 1 year ago

mjpieters/tqdm Fork of tqdm/tqdm
:zap: A Fast, Extensible Progress Bar for Python and CLI
  • environment.yml

Size: 5.71 MB - Last synced: 9 months ago - Pushed: 9 months ago

UFO-101/tqdm Fork of tqdm/tqdm
:zap: A Fast, Extensible Progress Bar for Python and CLI
  • environment.yml

Size: 5.37 MB - Last synced: 22 days ago - Pushed: 23 days ago

tqdm/tqdm
:zap: A Fast, Extensible Progress Bar for Python and CLI
  • environment.yml

Size: 5.71 MB - Last synced: 13 days ago - Pushed: 14 days ago

GBBBAS/core Fork of rtdip/core
Easy access to high volume, historical and real time process data for analytics applications, engineers, and data scientists wherever they are.
  • 10.1.0 environment.yml

Size: 23 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

nf-core/slamseq Fork of t-neumann/slamseq
SLAMSeq processing and analysis pipeline
  • 6.0.* environment.yml

Size: 4.46 MB - Last synced: 13 days ago - Pushed: 13 days ago

nf-core/pgdb Fork of bigbio/pgdb
The ProteoGenomics database generation workflow creates different protein databases for ProteoGenomics data analysis.
  • 8.1.1.* environment.yml

Size: 3.06 MB - Last synced: 13 days ago - Pushed: 13 days ago

rodalynbarce/core Fork of rtdip/core
Easy access to high volume, historical and real time process data for analytics applications, engineers, and data scientists wherever they are.
  • 10.1.0 environment.yml

Size: 21.6 MB - Last synced: 5 months ago - Pushed: 5 months ago