r-optparse | conda | Package Usage

oeg-upm/TPDL2022_FAIROs

1.6.6.* experiment1/research_object/environment.yml

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

ATpoint/sc_preprocess

Preprocessing of UMI-based scRNA-seq supporting spliced/unspliced count generation and feature barcoding experiments with alevin

environment.yml

Size: 63.5 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

qbic-pipelines/rnadeseq

Differential gene expression analysis and pathway analysis of RNAseq data

1.7.1.* environment.yml

Size: 62.6 MB - Last synced: 11 days ago - Pushed: 11 days ago

ulelab/clipplotr

A tool to facilitate comparative visualisation of CLIP data

1.6.6.* environment.yml

Size: 55.9 MB - Last synced: 6 months ago - Pushed: 6 months ago

zavolanlab/Dockerfiles

Dockerfile repository of the Zavolan Lab

1.6.0.* MAPP_base_R/1.0/environment.yaml

Size: 43.5 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago

lifebit-ai/traits-archived 📦

Workflow for collecting genetic traits information (heritability, genetic correlation) from GWAS summary statistics

environment.yml

Size: 128 KB - Last synced: about 1 month ago - Pushed: almost 3 years ago

morrislab/qapa

RNA-seq Quantification of Alternative Polyadenylation

environment.yml

Size: 2.79 MB - Last synced: 7 months ago - Pushed: 12 months ago

Clinical-Genomics-Lund/nextflow_rnaseqfus

Fusion genes identification pipeline

1.6.4.* container/environment.yml

Size: 2.16 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

metashot/docker

Metashot docker images

dockerfiles/anvio/7-1/environment.yml

Size: 1.35 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

casrssk/WGS-analysis-in-C_trachomatis

1.6.4 linux/sample/envs/environment.yml

Size: 7.39 MB - Last synced: 5 months ago - Pushed: about 2 years ago

ImperialCollegeLondon/covid19model

Code for modelling estimated deaths and cases for COVID19.

environment.yml
nature/environment.yml

Size: 64.8 MB - Last synced: 2 months ago - Pushed: about 3 years ago

brimittleman/Comparative_APA

Project for comparative APA- Start fall 2019

code/environment.yaml

Size: 245 MB - Last synced: 7 months ago - Pushed: over 3 years ago

MastodonC/witan.send

Modelling Special Educational Needs and Disability demand and costs

environment.yml

Size: 55.9 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

kircherlab/snakemake_wrappers

snakemake wrappers to share with others and to us ethem in multiple projects

plots/PR_ROC_curves_metric/environment.yaml
plots/ggcorrplot/environment.yaml
plots/gridplot/environment.yaml
plots/pre_re_f1_f2/environment.yaml

Size: 338 KB - Last synced: 11 months ago - Pushed: 11 months ago

eQTL-Catalogue/qcnorm

This pipeline will run QC measures of both genotype and phenotype data and will normalise quantified phenotypes

1.6.1.* containers/genotype_qc/environment.yml

Size: 196 KB - Last synced: 4 months ago - Pushed: 4 months ago

eQTLGen/DataQC

eQTL data QC pipeline for eQTLGen phase II project.

1.6.6.* environment.yml

Size: 13.2 MB - Last synced: 3 months ago - Pushed: 3 months ago

greenelab/pancancer

Building classifiers using cancer transcriptomes across 33 different cancer-types

1.4.4.* environment.yml

Size: 28.8 MB - Last synced: 7 months ago - Pushed: about 5 years ago

AnimalGenomicsETH/bovine-graphs

Integrate multiple genome assemblies into a pangenome graph

envs/environment.yml

Size: 23.4 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

bioinfo-pf-curie/ATAC-seq

Nextflow pipeline for ATAC-seq data analysis

1.6.4 environment.yml

Size: 3.41 MB - Last synced: 6 months ago - Pushed: over 1 year ago

lifebit-ai/phewas

Performs a PheWAS analysis & generates a Manhattan plot using the PheWAS R package

environment.yml

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

nlm-irp-jianglab/Evolink

:palm_tree: A Phylogenetic Approach for Rapid Identification of Genotype-Phenotype Associations in Large-scale Microbial Multi-species Data

1.7.1 environment.yml

Size: 251 MB - Last synced: 10 months ago - Pushed: 10 months ago

rki-mf1/vocal

Vocal is a simple Variants Of Concern ALert system script. Doc https://rki-mf1.github.io/vocal-doc/

1.7.1.* environment.yml

Size: 3.31 MB - Last synced: 2 months ago - Pushed: over 1 year ago

aleks96n/BioInfoKallisto

Benchmark kallisto against HISAT2 + featureCounts in eQTL mapping

1.6.1.* qtlmap/environment.yml

Size: 12.8 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago

lifebit-ai/simulate

Simulate genomic data on demand

1.6.6.* environment.yml

Size: 318 KB - Last synced: about 1 month ago - Pushed: about 1 year ago

vjayaman/Metrics-CGM-ECC

documentation/environment.yml

Size: 114 MB - Last synced: 14 days ago - Pushed: almost 2 years ago

lifebit-ai/prs

Polygenic Risk Scores Pipeline to calculate genetic risk score for any given phenotype/trait (using PRSice)

1.6.6.* environment.yml

Size: 57.6 MB - Last synced: about 1 month ago - Pushed: about 1 year ago

lifebit-ai/pcgr-nf

Pipeline to run pcgr tool on vcf file

1.6.6.* environment.yml

Size: 1.19 MB - Last synced: about 1 month ago - Pushed: about 1 year ago

AndreaMariani-AM/Docker

This repo contains github actions to build various Docker Images

1.6.6.* HiC-snakemake/environment.yml

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

ajodeh-juma/rvfv-amplicon-seq

A simple pipeline for Rift Valley fever virus consensus genome generation from amplicon sequencing

1.6.6.* environment.yml

Size: 11.4 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

omicsclass/biodocker

docker images for bioinformatics

1.6.4.* pop-evol-gwas/environment.yml

Size: 59.2 MB - Last synced: 12 months ago - Pushed: over 1 year ago

biominer-lab/omics-workflow-images

Docker images for omics workflow.

1.7.3 omics-cancer-subtype/environment.yml

Size: 33.8 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

scilifelab-lts/lts-workflows-sm-scrnaseq

1.4.4.* lts_workflows_sm_scrnaseq/environment.yaml

Size: 2.28 MB - Last synced: over 1 year ago

letaylor/snakemake-qtl

Snakemake pipeline for molecular trait QTL mapping

1.4.4 environment.yml

Size: 18.2 MB - Last synced: about 1 year ago - Pushed: over 4 years ago

ikmb/MAGScoT

MAGScoT - a MAG scoring and refinement tool

environment.yml

Size: 28.7 MB - Last synced: 10 months ago - Pushed: 10 months ago

NBISweden/sauron

Website is at:

1.6.* environment.yml

Size: 17.1 MB - Last synced: almost 1 year ago - Pushed: about 3 years ago

eQTL-Catalogue/qtlmap

Portable eQTL analysis and statistical fine mapping workflow used by the eQTL Catalogue

1.6.1.* environment.yml

Size: 15.5 MB - Last synced: 4 months ago - Pushed: 4 months ago

lifebit-ai/metagwas

1.6.6.* environment.yml

Size: 11 MB - Last synced: about 1 month ago - Pushed: about 1 year ago

crimBubble/ECCsplorer

The ECCsplorer is a bioinformatics pipeline for the automated detection of extrachromosomal circular DNA (eccDNA) from paired-end read data of amplified circular DNA.

environment.yml

Size: 15.9 MB - Last synced: 8 months ago - Pushed: 8 months ago

ryanlayerlab/layer_lab_chco

container/environment.yml

Size: 5.88 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

scilifelab-lts/sauron

1.6.* environment.yml

Size: 21 MB - Last synced: over 1 year ago

NatPombubpa/Qiime2_2022.8_binder

Qiime2_2022.8_binder test

1.7.3.* environment.yml

Size: 10.7 KB - Last synced: 9 months ago - Pushed: over 1 year ago

ggabernet/nf-core-airrflow Fork of nf-core/airrflow

Please use the original pipeline http://github.com/nf-core/airrflow

1.6.2.* environment.yml

Size: 8.18 MB - Last synced: 6 days ago - Pushed: 6 days ago

ParkerLab/ataqv-2019

1.6.0.* environment.yml

Size: 2.54 MB - Last synced: 11 months ago - Pushed: over 4 years ago

sebpott/dropseq_pipeline

environment.yaml

Size: 157 KB - Last synced: 7 months ago - Pushed: over 6 years ago

biocompute-objects/bco-ro-example-chipseq

Packaging a IEEE 2791 described BioCompute Object as RO-Crate, using nf-core/chipseq as example

1.6.6.* data/environment.yml

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

greenelab/tad_pathways_pipeline

Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs

1.4.4.* environment.yml

Size: 2.24 MB - Last synced: 7 months ago - Pushed: over 4 years ago

santiagorevale/pickrepprot

PickRepProt is a pipeline to predict a representative protein sequence per gene from transcriptomes for Drosophila species.

1.6.4.* environment.yml

Size: 18.6 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

This tool models the impact of a Bipartite Expression Drive (BED) on a population. The BED may be intended to spread 1) toxic proteins that sterilize BED-carrying females or 2) lethal seminal proteins that BED-carrying males transfer to females, killing them right after mating.

1.6.6.* environment.yml

Size: 283 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

mgalland/how-many-reads

Analyses related to RNA-seq experimental design: how many reads per sample, power, etc.

1.6.1.* environment.yaml

Size: 13 MB - Last synced: about 1 year ago - Pushed: about 4 years ago

wuaipinglab/sitePath_exec

Command line executable for sitePath

environment.yml

Size: 21.5 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

dippindots/mutational-signature-converter

Convert from mutational signature data to cbioportal file format

environment.yml

Size: 11.6 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago

gagneurlab/FRASER-analysis

Accompanying analysis code for the FRASER manuscript

environment.yml

Size: 4.67 MB - Last synced: 18 days ago - Pushed: over 3 years ago

Simontuk/sprint_covseq

Covseq-pipe nextflow

1.6.6.* environment.yml

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

NBISweden/excelerate-scRNAseq

Single RNA-seq data analysis with R (Finland, May, 2019)

1.6.* environment.yaml

Size: 342 MB - Last synced: 3 months ago - Pushed: almost 2 years ago

kennethabarr/CellrangerDemultiplex

Pipeline for aligning and demultiplexing scRNA-seq with cellranger

environment.yaml

Size: 254 KB - Last synced: about 1 year ago - Pushed: about 2 years ago

crickbabs/BABS-ATACSeqPE

This pipeline has been superceeded. Please use >>>

1.4.4.* environment.yaml

Size: 5.05 MB - Last synced: about 1 year ago - Pushed: over 5 years ago

BleekerLab/rnaseq-analysis-kallisto-sleuth

mRNA-Seq analysis using Kallisto and Sleuth

1.6.6 environment.yaml

Size: 177 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

asdcid/Genome_Assembly_Assessment

1.6.2 environment.yml

Size: 39.4 MB - Last synced: about 1 year ago - Pushed: over 4 years ago

tarunkhajuria42/atac-bioinfomatics

1.6.0.* environment.yml

Size: 1.04 MB - Last synced: about 2 months ago - Pushed: almost 5 years ago

lengfei5/nf_visium_kallisto

1.6.6.* environment.yml

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

qbicsoftware/r-container-lib

A collection of project-related Dockerfiles for a controlled R environment with defined R packages

1.6.6.* projects/QMKJB/environment.yml

Size: 150 KB - Last synced: 14 days ago - Pushed: about 3 years ago

Genomic-Medicine-Linkoping/nextflow_rnaseqfus

1.6.4.* container/environment.yml

Size: 2.11 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago

lengfei5/nf_atacseq

1.6.6.* environment.yml

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

bioinform/QBC_Single_Cell_Analysis_NGS

environment.yml

Size: 14.3 MB - Last synced: 7 months ago - Pushed: over 4 years ago

web-mev/mev-lrt

DESeq2 implementation of likelihood ratio test

1.7.3 docker/environment.yml

Size: 12.7 KB - Last synced: about 1 month ago - Pushed: 4 months ago

CshlSiepelLab/UniMod

environment.yml

Size: 279 KB - Last synced: 2 months ago - Pushed: over 1 year ago

kalebabram/GRUMPS

Genomic distance based Rapid Uncovering of Microbial Population Structures

environment.yml

Size: 7.48 MB - Last synced: 12 months ago - Pushed: 12 months ago

olavurmortensen/MF9155_env

Conda environment for course MF9155 at UiO.

1.6.4.* environment.yml

Size: 8.79 KB - Last synced: about 1 year ago - Pushed: over 4 years ago

ryanlayerlab/layer_lab_caw

NGS data analysis pipeline focused on somatic analysis

container/environment.yml

Size: 2.09 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

bioinfo-pf-curie/vegan

Variant calling pipeline for whole Exome and whole Genome sequencing cANcer data

1.6.6.* recipes/conda/environment.yml

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

kennethabarr/HCPipeline

environment.yaml

Size: 9.77 KB - Last synced: 11 months ago - Pushed: 11 months ago

GenomicsNX/excelerate-scRNAseq Fork of NBISweden/excelerate-scRNAseq

Single RNA-seq data analysis with R (Finland, May, 2019)

1.6.* environment.yaml

Size: 342 MB - Last synced: about 2 months ago - Pushed: about 4 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

1.6.6.* environment.yml

Size: 11.3 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago

GenomicsNX/atacseq-1 Fork of nf-core/atacseq

ATAC-seq peak-calling, QC and differential analysis pipeline

1.6.0.* environment.yml

Size: 3.95 MB - Last synced: about 2 months ago - Pushed: over 4 years ago

NPogo/scalepopgen_v2

1.7.3.* environment.yml

Size: 400 KB - Last synced: 10 months ago - Pushed: 12 months ago

ivelet/tools-iuc Fork of galaxyproject/tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission

1.6.6.* tools/scater/environment.yml

Size: 1.09 GB - Last synced: about 2 months ago - Pushed: about 2 months ago

BharatPanera/chipseq Fork of nf-core/chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

1.6.6.* environment.yml

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

sinanugur/scrna-workflow

scRNA workflow of Cellsnake

environment.yml

Size: 1.44 MB - Last synced: 3 months ago - Pushed: 3 months ago

merenlab/anvio

An analysis and visualization platform for 'omics data

.conda/environment.yaml

Size: 715 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

NPogo/scalepopgen_v3 Fork of BioInf2305/scalepopgen_v3

1.7.3.* environment.yml

Size: 58.1 MB - Last synced: 8 months ago - Pushed: 8 months ago

bihealth/snappy-pipeline

SNAPPY Nucleic Acid Processing in Python

1.6.4.* snappy_wrappers/wrappers/gcnv/annotate_gc/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/annotate_gc_wgs/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/call_cnvs_case_mode/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/call_cnvs_cohort_mode/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/contig_ploidy/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/contig_ploidy_case_mode/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/coverage/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/filter_intervals/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/joint_germline_cnv_segmentation/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/post_germline_calls/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/post_germline_calls_case_mode/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/preprocess_intervals/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/preprocess_intervals_wgs/environment.yaml
1.6.4.* snappy_wrappers/wrappers/gcnv/scatter_intervals/environment.yaml

Size: 7.57 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

baldikacti/chienlab-tnseq

1.7.3.* envs/environment.yaml

Size: 15 MB - Last synced: 6 months ago - Pushed: 6 months ago

Package Usage: conda: r-optparse

Dependent Repos 81