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https://bioconductor.org/packages/release/bioc/html/DESeq2.html

Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.

Proper citation: DESeq2 (RRID:SCR_015687) Copy   

•   Source: SciCrunch Registry

https://ccb.jhu.edu/software/stringtie/

Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .

Proper citation: StringTie (RRID:SCR_016323) Copy   

•   Source: SciCrunch Registry

https://www.rdocumentation.org/packages/DGCA/versions/1.0.2

Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix.

Proper citation: Differential Gene Correlation Analysis (RRID:SCR_020964) Copy   

•   Source: SciCrunch Registry

https://github.com/KrishnaswamyLab/MAGIC

Software tool for imputing missing values restoring structure of large biological datasets.Method that shares information across similar cells, via data diffusion, to denoise cell count matrix and fill in missing transcripts.

Proper citation: Markov Affinity based Graph Imputation of Cells (RRID:SCR_022371) Copy   

•   Source: SciCrunch Registry

https://github.com/greenelab/miQC

Software tool as flexible, probablistic metrics for quality control of scRNA-seq data. Adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. Data driven QC metric that jointly models proportion of reads mapping to mtDNA and number of detected genes with mixture models in probabilistic framework to predict which cells are low quality in given dataset.

Proper citation: miQC (RRID:SCR_022697) Copy   

•   Source: SciCrunch Registry

https://www.miti-consortium.org/

Consortium provides guidelines for highly multiplexed tissue images. Standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology. Data and metadata standards consistent with Findable, Accessible, Interoperable, and Reusable (FAIR) standards that guide data deposition, curation and release.

Proper citation: Minimum Information about Tissue Imaging (RRID:SCR_022830) Copy   

•   Source: SciCrunch Registry

http://cahub.cancer.gov/about/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. A national center for biospecimen science and standards to advance cancer research and treatment. It was created in response to the critical and growing need for high-quality, well-documented biospecimens for cancer research. The initiative builds on resources already developed by the NCI, including the Biospecimen Research Network and the NCI Best Practices for Biospecimen Resources, both of which were developed to address challenges around standardization of the collection and dissemination of quality biospecimens. caHUB will develop the infrastructure for collaborative biospecimen research and the production of evidence-based biospecimen standard operating procedures.

Proper citation: caHUB (RRID:SCR_009657) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/chea3/

Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries.

Proper citation: ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) Copy   

•   Source: SciCrunch Registry

https://kleintools.hms.harvard.edu/tools/spring.html

Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data.

Proper citation: SPRING (RRID:SCR_023578) Copy   

•   Source: SciCrunch Registry

http://www.hemonc.org

Medical wiki of interventions, regimens, and general information relevant to fields of hematology and oncology. Knowledge base for hematology and oncology providers, containing details about hematology/oncology drugs and treatment regimens. Any healthcare professional can sign up to contribute. Acuracy and completeness of content is overseen by Editorial Board.

Proper citation: HemOnc Knowledgebase (RRID:SCR_023436) Copy   

•   Source: SciCrunch Registry

https://het.io/search/

Web app that allows users to search for the most important paths connecting any two nodes in Hetionet.

Proper citation: Hetnet Connectivity Search (RRID:SCR_023630) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/kea3

Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations.

Proper citation: Kinase Enrichment Analysis 3 (RRID:SCR_023623) Copy   

•   Source: SciCrunch Registry

https://generanger.maayanlab.cloud/gene/A2M?database=ARCHS4

Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types.

Proper citation: GeneRanger (RRID:SCR_023622) Copy   

•   Source: SciCrunch Registry

https://targetranger.maayanlab.cloud/

Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines.

Proper citation: TargetRanger (RRID:SCR_023621) Copy   

•   Source: SciCrunch Registry

http://statistika.mfub.bg.ac.rs/interactive-linegraph/

Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions.

Proper citation: Interactive Line Graph (RRID:SCR_018334) Copy   

•   Source: SciCrunch Registry

https://cadd.gs.washington.edu/

Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome.

Proper citation: Combined Annotation Dependent Depletion (RRID:SCR_018393) Copy   

•   Source: SciCrunch Registry

https://geodacenter.github.io/

Software program for spatial analysis for non geographic information systems specialists. Includes functionality ranging from simple mapping to exploratory data analysis, visualization of global and local spatial autocorrelation, and spatial regression.

Proper citation: GeoDa (RRID:SCR_018559) Copy   

•   Source: SciCrunch Registry

https://delaney.shinyapps.io/FairSubset/

Web tool to choose representative subsets of data for use with replicates or groups of different sample sizes. Used to retain distribution information at single datum level and may be considered for standardized use in fair publishing practices.

Proper citation: FairSubset (RRID:SCR_019102) Copy   

•   Source: SciCrunch Registry

https://github.com/JamieHeather/stitchr

Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information.

Proper citation: Stitchr (RRID:SCR_022139) Copy   

•   Source: SciCrunch Registry

http://drugtargetontology.org/

Ontology of drug targets to be used as a reference for drug targets, with the longer-term goal of creating a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The project itself aims to develop a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families.

Proper citation: Drug Target Ontology (RRID:SCR_015581) Copy   

•   Source: SciCrunch Registry