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https://github.com/YingMa0107/CARD/

Software R package for spatial transcriptomics. Deconvolution method that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations.

Proper citation: Conditional AutoRegressive Deconvolution (RRID:SCR_026310) Copy   

•   Source: SciCrunch Registry

https://github.com/agshumate/Liftoff

Software genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely related species. Aligns genes from reference genome to target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript and gene. Used for accurate mapping of gene annotations.

Proper citation: Liftoff (RRID:SCR_026535) Copy   

•   Source: SciCrunch Registry

https://github.com/kaizhang/SnapATAC2

Software Python/Rust package for single-cell epigenomics analysis.

Proper citation: SnapATAC2 (RRID:SCR_026622) Copy   

•   Source: SciCrunch Registry

https://github.com/higlass/higlass

Web-based visual exploration and analysis of genome interaction maps.

Proper citation: HiGlass (RRID:SCR_026687) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/apeglm.html

Software package provides Bayesian shrinkage estimators for effect sizes for variety of GLM models, using approximation of posterior for individual coefficients.

Proper citation: apeglm (RRID:SCR_026951) Copy   

•   Source: SciCrunch Registry

https://github.com/Danko-Lab/dREG

Software tool for detecting regulatory elements using GRO-seq and PRO-seq.

Proper citation: dREG (RRID:SCR_027012) Copy   

•   Source: SciCrunch Registry

https://github.com/KrishnaswamyLab/PHATE

Software tool for visualizing high dimensional data using novel conceptual framework for learning and visualizing manifold to preserve both local and global distances.

Proper citation: PHATE (RRID:SCR_027119) Copy   

•   Source: SciCrunch Registry

https://github.com/Yonghao-Holden/TEProf3

Software pipeline to detect Transposable Elements transcripts. Used to identify TE-derived promoters and transcripts using transcriptomic data from multiple sources, including short-read RNA-seq data, long-read RNA-seq data and single cell RNA-seq data.

Proper citation: TEProf3 (RRID:SCR_027288) Copy   

•   Source: SciCrunch Registry

http://www.genome.gov/12514286

Current Topics in Genome Analysis lecture series consists of 13 lectures on successive Wednesdays, with a mixture of local and outside speakers covering the major areas of genomics. In this tenth edition of the series, rather than splitting the lectures into laboratory-based and computationally-based blocks, we have intermingled the lectures by general subject area. We hope that this approach conveys the idea that both laboratory- and computationally-based approaches are necessary in order to do cutting-edge biological research in the future. The lectures are geared at the level of first year graduate students, are practical in nature, and are intended for a diverse audience. Handouts will be provided for each lecture, and time will be available at the end of each lecture for questions and discussion. All lectures are held on Wednesday mornings from 9:30 a.m. to 11:00 a.m. in the Lipsett Amphitheatre of the National Institutes of Health Clinical Center (Building 10). Course Directors: Andy Baxevanis, Ph.D., Eric Green, M.D., Ph.D., Tyra Wolfsberg, Ph.D. Lectures in this series will be available on the GenomeTV channel of YouTube viewing shortly after the live lecture and also includes all of the handouts. Lectures will not be Webcast live. The lecture series archives (available from 2005-) covers important milestones in genetics. CME Credits: This activity has been approved for AMA PRA Category 1 Credits. The intended audience includes clinicians, clinical geneticists, social and behavioral scientists, genetic counselors, those involved with genetics and public policy, health educators, and other biomedical and clinical scientists with an interest in genetics, genomics and personalized medicine. No prior expertise on the part of the audience will be required and the lecturers will be instructed to provide any relevant background as part of their lectures.

Proper citation: Current Topics in Genome Analysis (RRID:SCR_006475) Copy   

•   Source: SciCrunch Registry

https://github.com/zhoujt1994/scHiCluster

Software Python package for single-cell chromosome contact data analysis. It includes the identification of cell types (clusters), loop calling in cell types, and domain and compartment calling in single cells. Facilitates visualization and comparison of single-cell 3D genomes.

Proper citation: scHiCluster (RRID:SCR_027854) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/tximeta.html

Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility.

Proper citation: tximeta (RRID:SCR_028005) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/somalier

Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches.

Proper citation: somalier (RRID:SCR_028167) Copy   

•   Source: SciCrunch Registry

https://github.com/pacificbiosciences/trgt

Software tool for plotting pureTarget repeat panel results (generates waterfall plot). Used for Tandem repeat genotyping and visualization from PacBio HiFi data.

Proper citation: TRGT (RRID:SCR_028810) Copy   

•   Source: SciCrunch Registry

http://mged.sourceforge.net/ontologies/MGEDontology.php

An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed.

Proper citation: MGED Ontology (RRID:SCR_004484) Copy   

•   Source: SciCrunch Registry

http://sequenceontology.org/

A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl.

Proper citation: SO (RRID:SCR_004374) Copy   

•   Source: SciCrunch Registry

http://bix.ucsd.edu/projects/singlecell/

Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria.

Proper citation: Velvet-SC (RRID:SCR_004377) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/ASprofile/

A suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.

Proper citation: ASprofile (RRID:SCR_001833) Copy   

•   Source: SciCrunch Registry

http://mousecyc.jax.org/

A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database.

Proper citation: MouseCyc (RRID:SCR_001791) Copy   

•   Source: SciCrunch Registry

https://github.com/hms-dbmi/spp

R analysis and processing package for Illumina platform Chip-Seq data.

Proper citation: SPP (RRID:SCR_001790) Copy   

•   Source: SciCrunch Registry

http://provean.jcvi.org/

A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.

Proper citation: PROVEAN (RRID:SCR_002182) Copy   

•   Source: SciCrunch Registry