ncbi/Co-SELECT

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ncbi/Co-SELECT

ncbi

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This repository contains the source code of Co-SELECT, a computational tool to analyze the results of in vitro HT-SELEX experiments for TF-DNA binding to show the role of DNA shape in TF-DNA binding by using a novel method of deconvoluting the contributions of DNA sequence and DNA shape on the binding.

sra-tools

GeneGPT

Code and data for GeneGPT.

datasets

NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

Jupyter Notebook

pgap

NCBI Prokaryotic Genome Annotation Pipeline

Common Workflow Language

amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

PubReader

A new way to view journal articles

icn3d

web-based protein structure viewer and analysis tool interactively or in batch mode

TPMCalculator

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

MedCPT

Code for MedCPT, a model for zero-shot biomedical information retrieval.

dbsnp

Jupyter Notebook

ngs

NGS Language Bindings

SKESA

SKESA assembler

blast_plus_docs

ngs-tools

vadr

Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

fcs

Foreign Contamination Screening caller scripts and documentation

ncbi-vdb

gprobe

client app for the gRPC health-checking protocol

robotframework-pageobjects

Implementation of the Page Object pattern with Robot Framework and selenium. Also facilitates page object pattern independent of Robot Framework

SSDraw

Jupyter Notebook

BAMscale

BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.

clinvar

ClinVar aggregates information about genomic variation and its relationship to human health. Contact us at '[email protected]' with any questions or comments.

rapt

Read Assembly and Annotation Pipeline Tool

ncbi-cxx-toolkit-public

NCBI C++ Toolkit package sources

JATSPreviewStylesheets

JATS Preview Stylesheets

docker

sra-human-scrubber

An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.

elastic-blast

ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective

BioConceptVec

Jupyter Notebook

dbvar

AIONER

magicblast

JUDI

This repository contains the source code of JUDI, a workflow management system for developing complex bioinformatics software with many parameter settings. Bioinformatics pipeline: Just Do It!

sratoolkit

SRAToolkit has been REPLACED - see README

bert_gt

egapx

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

osiris

OSIRIS is a public domain quality assurance software package that facilitates the assessment of multiplex short tandem repeat (STR) DNA profiles based on laboratory-specific protocols. OSIRIS evaluates the raw electrophoresis data contained in .fsa or .hid files using an independently derived mathematically-based sizing algorithm. OSIRIS currently supports ABI capillary analytical platforms and numerous commercially available marker kits including all CODIS-compliant kits as well as those favored by biomedical laboratories.

pm4ngs

Project Manager for NGS data analysis

BioREx

cwl-ngs-workflows-cbb

A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis

Common Workflow Language

consul-announcer

Service announcer for Consul (https://www.consul.io/).

scPopCorn

A python tool to do comparative analysis of mulitple single cell datasets.

Jupyter Notebook

workshop-ncbi-data-with-python

BioRED

cxx-toolkit

EvoGeneX

This repository contains the source code of the R package for EvoGeneX, a software to infer the mode of evolution from the gene expression data.

tree-tool

Incremental building of phylogenetic distance trees

GNorm2

pipelines

Common Workflow Language

tmVar3

graf

Genetic Relationship And Fingerprinting

ribovore

biomedical-citation-selector

PMCXMLConverters

PMC XML Converters

gaptools

dbGaP data validation tool repo

AF2_benchmark

Jupyter Notebook

sars2variantcalling

The NCBI SARS-CoV-2 Variant Calling (SC2VC) Pipeline allows calling high-confidence variants from SARS-CoV-2 NGS data in a standardized format

ICITY

fcs-gx

Foreign Contamination Screening - GX source code

blast-cloud

Documentation for NCBI BLAST AMI

RepairSig

finagle-consul

Service discovery for Finagle cluster with Consul.

NetREX

python-libpq-dev

packit

Python packaging in declarative way (wrapping pbr to make it flexible)

workshop-asm-ngs-2022

Pre-conference workshop for ASM NGS 2022

elastic-blast-demos

ElasticBLAST demos

Jupyter Notebook

PSSS-Bytes2Biology

Petabyte Scale Sequence Search Initiative

HYDROID

Python package for analyzing hydroxyl-radical footprinting experiments of DNA-protein complexes

ncbi-drs

GA4GH DRS Service

ncbi-logging

Log monitoring and gathering infrastructure to feed analytics

cwl-demos

CWL demonstration pipelines

Common Workflow Language

SpeciesAssignment

SpeciesAssignment

niso-jats

dual_fold_coevolution

mti

NLM Medical Text Indexer (MTI)

DbGaP-FHIR-API-Docs

The documentation repository for the dbGaP FHIR API.

Jupyter Notebook

mtix

ML based NLM Medical Text Indexer

ITSx

Not the official ITSx repository, please visit https://microbiology.se/software/itsx/

deeplensnet

gtax

biomedical-citation-selector-trainer

Biomedical Citation Selector Trainer

SuPER

AceView

Acedb object oriented database engine and AceView/MAGIC RNA_seq pipeline, NCBI/NLM/NIH

stxtyper

StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.

ncbi-xmlwrapp

NCBI’s fork of “xmlwrapp” -- a C++ wrapper for libxml2/libxslt libraries

ncbi-cxx-toolkit-conan

NCBI C++ Toolkit package recipe

biocreative_litcovid

Evaluation scripts of the Biocreative LitCovid track

NETPHIX

A computational tool to identify mutated subnetworks that are associated with a continuous cancer phenotype

SRPRISM

deflake

deflake.py Helps debug a non determinate test (or any flaky program) by running it until it exits with a non-zero exit code.

ncbi_doc_template

Solr-Plugins

Assorted plugins for Solr

ncbi_css_standards

datadicer

GeneSigNet

nlm-dtd

CoV-Dist

cloud-transcriptome-annotation

Time and cost comparison on GCP and AWS for transcriptome annotation

Jupyter Notebook

elastic-blast-docs

ElasticBLAST documentation