Ecosyste.ms: Repos

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

Package Usage: conda: entrez-direct

View more package details: https://packages.ecosyste.ms/registries/anaconda.org/packages/entrez-direct

Dependent Repos 44

ifremer-bioinformatics/samba
Standardized and Automated MetaBarcoding Analyses workflow (Mirror)
  • 11.0 containers/qiime2-2019.10/environment.yml

Size: 109 MB - Last synced: 11 months ago - Pushed: 11 months ago

adenger/subpred3
Code for the manuscript "Optimized data set and feature construction for substrate prediction of membrane transporters"
  • 16.2 environment.yml

Size: 50.6 MB - Last synced: 21 days ago - Pushed: 10 months ago

lfnothias/qiime2
  • 13.9.* environment.yml

Size: 21.5 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

rchapman2000/de-novo-assembly-pipeline
  • 16.2 environment.yml

Size: 60.5 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

ModernisingMedicalMicrobiology/assembly_comparison
  • environment.yml

Last synced: over 1 year ago

MPI-SHH-SummerSchool/dag-material
  • 13.9.* Hands on Introduction to Ancient Microbiome Analysis/environment.yml

Size: 489 MB - Last synced: 9 months ago - Pushed: over 2 years ago

evoosa/16S_bacteria_detector
Gets the frequency of bacterias for 16S RRNA sequences using the available algorithms
  • 13.3 src/environment.yml

Size: 97.4 MB - Last synced: about 1 year ago - Pushed: about 3 years ago

leipzig/metadata-in-rcr
code and data related to "The Role of Metadata in Reproducible Computational Research"
  • .binder/environment.yml

Size: 54.5 MB - Last synced: 13 days ago - Pushed: over 2 years ago

PavlidisLab/rnaseq-pipeline
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
  • environment.yml

Size: 43.5 MB - Last synced: 4 days ago - Pushed: 4 days ago

CellProfiling/FucciSingleCellSeqPipeline
Cell cycle analysis of single-cell proteomic and transcriptomic data for the FUCCI cell model -- RNA-Seq analysis pipeline
  • workflow/envs/environment.yaml

Size: 116 KB - Last synced: 7 months ago - Pushed: 7 months ago

LPCDRP/hybran
Hybrid reference-based and ab initio annotation of prokaryotic genomes https://lpcdrp.gitlab.io/hybran/
  • environment.yml

Last synced: 11 months ago

mcveanlab/Corticall
Germline DNM caller based on LdBG assembly of pathogens
  • 7.70.* cromwell/docker/cloud-downloader/environment.yml

Size: 128 MB - Last synced: 8 months ago - Pushed: about 4 years ago

bokulich-lab/advanced-comp-bio-tutorial
Hands-on demonstration of 16S rRNA gene sequence analysis for SysBio Advanced Block Course 2022
  • 16.2 environment.yml

Size: 77.9 MB - Last synced: 12 months ago - Pushed: 12 months ago

kaspermunch/sap
Statistical Assignment Package
  • 16.2 environment.yml

Size: 51.1 MB - Last synced: 7 months ago - Pushed: about 1 year ago

Bernt/MITOS
MITOS
  • 15.6.* environment.yaml

Last synced: 15 days ago

jbloomlab/SARS-CoV-2-RBD_DMS_Omicron
DMS of the Omicron BA.1 and BA.2 RBDs
  • 13.9.* environment.yml

Size: 48.7 MB - Last synced: 10 months ago - Pushed: about 1 year ago

jbloom/PRJNA692319_public
Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2
  • 16.2.* environment.yml

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: about 2 years ago

omicsclass/biodocker
docker images for bioinformatics
  • 13.3.* ampliseq-q2/environment.yml

Size: 59.2 MB - Last synced: 11 months ago - Pushed: over 1 year ago

ctlab/GScour
Genome-wide detection of positive selection
  • 13.9 environment.yml

Size: 1.89 MB - Last synced: 28 days ago - Pushed: 11 months ago

mr-eyes/denovo-rnaseq
De novo assembly, Differential gene expression, and annotation workflow
  • 16.2 environment.yml

Size: 1.79 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

NatPombubpa/Qiime2_2022.8_binder
Qiime2_2022.8_binder test
  • 16.2.* environment.yml

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

jbloomlab/SARS2-mut-spectrum
Mutational spectrum of SARS-CoV-2
  • 16.2.* environment.yml

Size: 11.8 MB - Last synced: 16 days ago - Pushed: over 1 year ago

deconvolute/subgenome
Identification of druggable genes in pathogenic bacteria – subtractive genomics approach
  • 16.2 environment.yml

Size: 10.6 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

bshifaw/long-read-pipelines Fork of broadinstitute/long-read-pipelines
Long read production pipelines
  • 13.9 docker/lr-cloud-downloader/environment.yml

Size: 94.9 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

jbloomlab/SARS-CoV-2-RBD_DMS_variants
  • 13.9.* environment.yml

Size: 143 MB - Last synced: 6 months ago - Pushed: about 1 year ago

dms-vep/dms-vep-pipeline
Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
  • 16.2.* environment.yml

Size: 244 MB - Last synced: 26 days ago - Pushed: 8 months ago

fieldima/adequacy_of_PCMs Fork of phylo-lab-usc/fiels_workbench
This repository contains all the scripts for analyzing the adequacy of the most commonly used phylogenetic comparative models for gene expression datasets.
  • 16.2 Normalization_Reanalysis/environment.yml

Size: 350 MB - Last synced: 11 months ago - Pushed: over 1 year ago

healthyPlant/PhytoPipe
  • environment.yaml

Size: 114 MB - Last synced: 4 months ago - Pushed: 4 months ago

SteMIDIfactory/P-DOR
Quick and easy outbreak reconstruction pipeline
  • 16.2 environment.yml

Size: 37.7 MB - Last synced: 3 months ago - Pushed: 8 months ago

jbloom/SARS-CoV-2_Shen_et_al
  • 13.9.* environment.yml

Size: 930 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

duncanberger/nxf-BATQual
Bacterial genome assembly, annotation and typing pipeline.
  • 16.2 environment.yaml

Size: 321 KB - Last synced: 10 months ago - Pushed: 10 months ago

liaoherui/StrainAnalyze
StrainAnalyze: a user-friendly bioinformatics pipeline used to analyze given identified bacterial strains in short reads.
  • 16.2 environment.yaml

Size: 14.6 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

lisakmalins/opentope
An open-source pipeline to discover universal epitopes for vaccines.
  • 13.3.* environment.yaml

Size: 1.4 MB - Last synced: 9 months ago - Pushed: about 4 years ago

neavemj/mappd
Metagenomic Analysis Pipeline for Pathogen Discovery
  • 11.0 environment.yaml

Size: 924 KB - Last synced: 8 months ago - Pushed: 8 months ago

IanSudbery/alvarez_et_al
Code and other scripts for Alvarez-Beneyas et al 2020
  • 13.9 environment.yml

Size: 41.2 MB - Last synced: 9 months ago - Pushed: over 2 years ago

greenkidneybean/bchb524_final
  • 10.0 environment.yml

Size: 174 KB - Last synced: about 1 year ago - Pushed: over 4 years ago

jaswindersingh2/RNAcmap2
Improved RNA homology detection and alignment by automatic iterative search in an expanded database
  • 15.6 environment.yaml

Size: 345 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

bfairkun/design-mpeseq-primers
For designing RT primers with blast search, tm constraints, etc
  • 11.0 environment.yaml

Size: 28.3 KB - Last synced: 7 months ago - Pushed: almost 5 years ago

jackkamm/snippy-false-negatives
  • 10.2 environment.yaml

Size: 4.88 KB - Last synced: about 1 year ago - Pushed: over 5 years ago

yangmqglobe/dlpipe
一个全自动，可断点续传的从 GEO 数据库下载原始 FASTQ 文件的流程。
  • 16.2.* environment.yml

Size: 6.84 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

lifebit-ai/nf-fastq-dumper
Dump all fastqas from SRA project ID - just that
  • 7.70.* environment.yml

Size: 1000 Bytes - Last synced: 25 days ago - Pushed: over 4 years ago

jbloomlab/SARS2-prot-sub-counts
Counts of protein substitutions on SARS-CoV-2 global UShER tree
  • 16.2.* environment.yml

Size: 1.82 MB - Last synced: 6 months ago - Pushed: over 1 year ago

ErasmusMC-Bioinformatics/WeFaceNano
Nanopore plasmid pipeline (FAST5 basecalling, assembly, plasmid identification and antimicrobial resistance genes identification).
  • 13.8 environment.yml

Size: 6.78 MB - Last synced: about 1 month ago - Pushed: about 3 years ago

mwang87/GNPS_Volatility_Notebooks
  • 13.3.* environment.yml

Size: 14.6 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

jhgille2/cs590_2023
Random files for CS590 Spring 2023
  • 16.2 e9/environment.yml

Size: 39.7 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

tmbuza/imap-sample-metadata-og
Downloading metadata from SRA database, exploration and profiling
  • 16.2.* workflow/envs/environment.yml

Size: 83.1 MB - Last synced: about 2 months ago - Pushed: about 1 year ago

gaojunxuan/bcb330_project
  • 16.2 environment.yml

Size: 17.2 MB - Last synced: about 1 year ago - Pushed: about 2 years ago

qbicsoftware/r-container-lib
A collection of project-related Dockerfiles for a controlled R environment with defined R packages
  • 10.2 projects/QTEST/environment.yml

Size: 150 KB - Last synced: 2 days ago - Pushed: about 3 years ago

oscarlr/IGenotyper_depr
  • 11.0 environment.yml

Size: 4.9 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago

aszaryk/convertconda
  • 13.9.* environment.yml

Size: 1000 Bytes - Last synced: 11 months ago - Pushed: about 1 year ago

socialgene/sgnf
SocialGene's Nextflow Pipeline
  • 16.2 dockerfiles/sgpy/sgpy_base/environment.yaml

Size: 2.82 MB - Last synced: 3 months ago - Pushed: 3 months ago

TRON-Bioinformatics/easyfuse-src
EasyFuse source code to build python package
  • 16.2 environment.yml

Size: 105 MB - Last synced: 9 months ago - Pushed: 9 months ago

socialgene/sgpy
Python package for creating and interacting with graph databases of protein domains and their genome coordinates
  • 16.2 docker/sgpy_base/environment.yaml

Size: 17.1 MB - Last synced: 12 days ago - Pushed: 13 days ago

robert-altwasser/umi-processing
  • 16.2 env/environment.yml

Size: 340 KB - Last synced: 5 months ago - Pushed: 6 months ago

appliedbinf/pima-docker2
Volume based Pima Docker
  • 16.2 Internal/environment.yml

Size: 10.7 MB - Last synced: 6 months ago - Pushed: 6 months ago

unicorn-23/GwasWA
  • 16.2 environment.yml

Size: 75.5 MB - Last synced: 5 months ago - Pushed: 5 months ago

tmbuza/imap-download-sra-reads
Downloading fastq reads from SRA database
  • 16.2.* workflow/envs/environment.yml

Size: 102 MB - Last synced: 18 days ago - Pushed: 18 days ago

aemann01/ads_plaque
Metatranscriptomics and the arginine deiminase pathway
  • 16.2.* 03-diff_abundance/environment.yml

Size: 16.1 MB - Last synced: 2 months ago - Pushed: 2 months ago

dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS
  • 13.9.* library_design/environment.yml

Size: 537 MB - Last synced: 26 days ago - Pushed: 28 days ago

celinehohzm/intron_pos_conserve
tracking recent intron gains/loss
  • environment.yml

Size: 7.2 MB - Last synced: 2 months ago - Pushed: 2 months ago

jhuapl-bio/mytax
mytax is a tool for building custom taxonomies, useful for nucleotide sequence classification
  • 16.2.* environment.yml

Size: 42.6 MB - Last synced: 21 days ago - Pushed: about 2 months ago

IdoBar/3030NSC-workshops-binder
  • .binder/environment.yml

Size: 1.2 MB - Last synced: 27 days ago - Pushed: 27 days ago

nf-core/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
  • 16.2.* modules/nf-core/entrezdirect/esearch/environment.yml
  • 16.2.* modules/nf-core/entrezdirect/esummary/environment.yml
  • 16.2.* modules/nf-core/entrezdirect/xtract/environment.yml

Size: 146 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

sib-swiss/NGS-introduction-training
SIB course that introduces analysis of NGS data
  • >=15 Docker/vscode/environment.yml

Size: 46.7 MB - Last synced: 26 days ago - Pushed: 27 days ago

dms-vep/flu_h3_hk19_dms
Analysis of a multi-mutant, barcoded influenza H3 library in the A/HongKong/45/2019 background.
  • 16.2.* environment.yml

Size: 1020 MB - Last synced: 23 days ago - Pushed: 24 days ago

deepomicslab/LocalHGT
Detect complete horizontal gene transfer (HGT) event rapidly and accurately from complex metagenomics data.
  • 16.2 environment.yml

Size: 65.8 MB - Last synced: 19 days ago - Pushed: 19 days ago

jbloomlab/SARS2-mut-fitness
Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates
  • 16.2.* environment.yml

Size: 417 MB - Last synced: 16 days ago - Pushed: 19 days ago

jbloomlab/SARS2-cocktail-vax
Cocktail of SARS-CoV-2 spikes with predicted future mutation
  • 16.2.* environment.yml

Size: 31.3 KB - Last synced: 15 days ago - Pushed: 15 days ago

LPCDRP/hybran
comparative prokaryotic genome annotation
  • environment.yml

Size: 6.67 MB - Last synced: 7 days ago - Pushed: 7 days ago

dms-vep/dms-vep-pipeline-3
Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
  • 16.2.* environment.yml

Size: 222 MB - Last synced: 3 days ago - Pushed: 3 days ago