metamaden/seq_answers

Sequencing data preprocessing

Language: R - Size: 1.44 MB - Last synced: 7 days ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

vanheeringen-lab/seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Language: Python - Size: 1.39 GB - Last synced: 7 days ago - Pushed: 4 months ago - Stars: 146 - Forks: 26

adamklie/predictMEE

Predicting missing metadata with recurrent neural network (RNNs) based entity extraction

Language: Jupyter Notebook - Size: 83.1 MB - Last synced: 8 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

CDCgov/seqsender

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

Language: Python - Size: 83.9 MB - Last synced: 8 days ago - Pushed: 9 days ago - Stars: 29 - Forks: 9

wwood/kingfisher-download

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

Language: Python - Size: 9.92 MB - Last synced: 10 days ago - Pushed: 4 months ago - Stars: 228 - Forks: 38

saketkc/pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

Language: Python - Size: 7.01 MB - Last synced: about 18 hours ago - Pushed: 8 months ago - Stars: 297 - Forks: 49

showteeth/scfetch

Access and Format Single-cell RNA-seq Datasets from Public Resources

Language: R - Size: 4.52 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 23 - Forks: 2

nf-core/fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

Language: Nextflow - Size: 3.82 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 125 - Forks: 65

aofarrel/SRANWRP

Wraps up some SRA-related utilities

Language: WDL - Size: 4.65 MB - Last synced: 18 days ago - Pushed: 19 days ago - Stars: 2 - Forks: 3

bcgsc/rsempipeline

A pipeline for running rsem analysis on thousands of samples

Language: Python - Size: 331 KB - Last synced: 28 days ago - Pushed: over 5 years ago - Stars: 1 - Forks: 2

mr-eyes/sra_size_plot

Up-to-date SRA growth size visualization

Language: Python - Size: 1.06 MB - Last synced: 28 days ago - Pushed: 28 days ago - Stars: 1 - Forks: 0

arcones/sra-collector

Collect NIH NCBI SRA metadata of several GEO studies in one search

Language: Python - Size: 59.1 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

quantori/FastqHeat

Python wrapper created to help download metagenomic data from SRA or ENA databases

Language: Python - Size: 273 KB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

nuno-agostinho/psichomics

Interactive R package to quantify, analyse and visualise alternative splicing

Language: R - Size: 56.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 33 - Forks: 12

pepkit/geofetch

Builds a PEP from SRA or GEO accessions

Language: Jupyter Notebook - Size: 913 KB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 40 - Forks: 5

rachadele/download-geo-fastqs

Download fastqs or supplementary files from GEO and upload to hca-util bucket

Language: Shell - Size: 77.1 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

uc-bd2k/GREP2

GEO RNA-seq Experiments Processing Pipeline

Language: R - Size: 2.11 MB - Last synced: 7 days ago - Pushed: over 4 years ago - Stars: 20 - Forks: 10

CDCgov/tostadas

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Language: Python - Size: 35.1 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 17 - Forks: 6

zkCohort/sra-wasm

An SRA library through which web assembly is provided as an interface to generate SRA public and private keys client side

Language: Rust - Size: 205 MB - Last synced: 23 days ago - Pushed: 7 months ago - Stars: 1 - Forks: 0

louiejtaylor/grabseqs

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

Language: Python - Size: 281 KB - Last synced: 4 months ago - Pushed: about 4 years ago - Stars: 101 - Forks: 15

PathoGenOmics-Lab/getNCBImetadata

🪛 Fetch ncbi metadata for sra and assemblies

Language: Python - Size: 38.1 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

gavieira/mitofree 📦

Automated mitochondrial genome assembly using SRA public data

Language: Perl - Size: 25.3 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

NCBI-Hackathons/MetadataTable

Work on and around an interactive metadata table for project identification

Language: Python - Size: 113 KB - Last synced: about 1 month ago - Pushed: about 6 years ago - Stars: 5 - Forks: 2

wucc009/Platelet_transcriptome_fastq_data_processing

血小板转录组fastq数据处理

Language: Shell - Size: 22.5 KB - Last synced: 4 months ago - Pushed: 12 months ago - Stars: 2 - Forks: 0

linsalrob/partie

PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied annotations of the data sets can not be trusted, and so PARTIE allows automatic separation of the data.

Language: Perl - Size: 245 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 22 - Forks: 5

UnseenBio/sra-demo-benchmark

A demo workflow showing download, extraction, and compression of sequences from SRA.

Language: HTML - Size: 3.99 MB - Last synced: 7 months ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

FOI-Bioinformatics/metaquest

MetaQuest is a robust and user-friendly command-line toolkit designed to simplify and streamline the analysis of metagenomic data. From summarizing the presence of specific genomes to visualizing complex datasets, MetaQuest offers an array of tools to help researchers uncover insights from their metagenomic datasets.

Language: Python - Size: 123 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 1 - Forks: 0

Majid-Soheili/BMDSRA

Sequence Read Archive Classification

Language: Python - Size: 44.7 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 1

cyverseuk/NCBI_SRA_import

Language: Shell - Size: 4.88 KB - Last synced: 10 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

lucasmenendez/gopsi

Simple Private Set Intersection implemented in pure Go.

Language: Go - Size: 54.7 KB - Last synced: 11 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

NCBI-Hackathons/ViruSpy

A pipeline for viral identification from metagenomic samples

Language: Shell - Size: 8.68 MB - Last synced: about 1 month ago - Pushed: over 6 years ago - Stars: 25 - Forks: 4

davetang/sars_cov_2

Bioinformatics analysis of SARS-CoV-2

Language: Perl - Size: 81.8 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 15 - Forks: 6

nozerorma/transcriptomic-final-exercise Fork of bioinfo-lessons/transcriptomic-final-exercise

General RNA-seq pipeline for SRA samples

Language: HTML - Size: 15.8 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

mbernste/hypothesis-driven-SRA-queries

Find structured-datasets from within the Sequence Read Archive

Language: Jupyter Notebook - Size: 29.3 MB - Last synced: 10 months ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 1

rohitsuratekar/CardioPipeLine

Pipeline for RNA-seq analysis

Language: Python - Size: 208 KB - Last synced: over 1 year ago - Pushed: over 3 years ago - Stars: 7 - Forks: 0

hunglin59638/juno

read data generator

Language: Python - Size: 16.3 MB - Last synced: 8 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

schosio/GUFETCH

A GUI tool to download SRA files

Language: Shell - Size: 38.1 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

rhodesch/scRNA-seq

Single Cell RNA-Seq Workflow

Language: R - Size: 1.53 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

kopalgarg/RNA-seq-SRA

Language: wdl - Size: 6.84 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

plger/SRAdownload

Bash script to download fastq files from the SRA, with priority to european servers

Language: Shell - Size: 23.4 KB - Last synced: 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

genomeud/SRA-ome

Code for systematically classify data in SRA according to all the taxa present in the reads (SRA-metagenome)

Language: C++ - Size: 461 MB - Last synced: 10 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

vjcitn/omicidxClient

R functions for querying Sean Davis' omicidx system

Language: JavaScript - Size: 1.13 MB - Last synced: 18 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

YogiOnBioinformatics/ChIP-Seq-Analysis-Nanog-and-H3K27Ac

Independent project I undertook to perform a full ChIP-Seq analysis of the transcription factor Nanog in Zebrafish embryos.

Size: 348 KB - Last synced: 27 days ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

linsalrob/sra-cloud

Tools, tricks, tips, and uses for SRA in the cloud

Size: 3.91 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

TheJacksonLaboratory/cgp_sra_upload

Batch upload bam files to NCBI SRA using aspera

Language: Shell - Size: 6.84 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

lcolladotor/recount-brain-bog19

Poster for Biology of Genomes 2019 (#bog19) on recount-brain

Language: HTML - Size: 3.33 MB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 3

pmenzel/biq

Tool for indexing and querying back-splice junctions of circular RNAs (circRNAs) in RNA-Seq datasets

Language: JavaScript - Size: 11.8 MB - Last synced: 7 months ago - Pushed: about 5 years ago - Stars: 2 - Forks: 0

mervyn-mccreight/coinflip

Implement a non-server dependent coin flipper client as part of a IT-Security project in university.

Language: Java - Size: 3.37 MB - Last synced: over 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

rhodesch/ncbi_geo_submission

Language: Shell - Size: 3.91 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

Imamachi-n/AutoNGS

Automatic NGS data analysis from SRA download to the quantification of RNAs.

Language: Python - Size: 34.2 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 1 - Forks: 0