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http://www.sanger.ac.uk/science/tools/seqtools

Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites.

Proper citation: Blixem (RRID:SCR_015994) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/amap-align/

Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method.

Proper citation: AMAP (RRID:SCR_015969) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/fermi-lite

Standalone C library as well as a command-line tool for assembling Illumina short reads in small regions. It is an overlap-based assembler used in sequencing to retain heterozygous events and to assemble diploid regions for the purpose of variant calling.

Proper citation: fermi-lite (RRID:SCR_016112) Copy   

•   Source: SciCrunch Registry

https://www.archrproject.com/

Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing.

Proper citation: ArchR (RRID:SCR_020982) Copy   

•   Source: SciCrunch Registry

http://omics.informatics.indiana.edu/AbundantOTU/

Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset.

Proper citation: AbundantOTU+ (RRID:SCR_016527) Copy   

•   Source: SciCrunch Registry

http://www.lincsproject.org/

Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center.

Proper citation: LINCS Project (RRID:SCR_016486) Copy   

•   Source: SciCrunch Registry

https://github.com/rondolab/MR-PRESSO

Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing.

Proper citation: MR-PRESSO (RRID:SCR_023697) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/alkesgroup/Eagle/

Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.

Proper citation: Eagle (RRID:SCR_015991) Copy   

•   Source: SciCrunch Registry

https://github.com/marbl/Mash

Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.

Proper citation: Mash (RRID:SCR_019135) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/rtracklayer/

Software R package for interfacing with genome browsers.Supports integration of existing genome browsers with experimental data analyses performed in R. R interface to genome annotation files and UCSC genome browser.

Proper citation: rtracklayer (RRID:SCR_021325) Copy   

•   Source: SciCrunch Registry

https://github.com/stephens999/ashr

Software R package for adaptive shrinkage. Implements Empirical Bayes approach for large scale hypothesis testing and false discovery rate estimation.

Proper citation: Adaptive Shrinkage in R (RRID:SCR_023486) Copy   

•   Source: SciCrunch Registry

https://github.com/raphael-group/chisel

Software tool to infer allele and haplotype specific copy numbers in individual cells from low coverage single cell DNA sequencing data. Integrates weak allelic signals across individual cells, powering strength of single cell sequencing technologies to overcome weakness. Includes global clustering of RDRs and BAFs, and rigorous model selection procedure for inferring genome ploidy that improves both inference of allele specific and total copy numbers.

Proper citation: CHISEL (RRID:SCR_023220) Copy   

•   Source: SciCrunch Registry

http://zfishbook.org/

Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates.

Proper citation: zfishbook (RRID:SCR_006896) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/bioc/html/HiCDCPlus.html

Software package for Hi-C/HiChIP interaction calling and differential analysis using efficient implementation of HiC-DC statistical framework. Enables principled statistical analysis of Hi-C and HiChIP data sets. Enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP

Proper citation: HiCDCPlus (RRID:SCR_025317) Copy   

•   Source: SciCrunch Registry

https://github.com/pjedge/longshot

Software variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). Enables accurate variant calling in diploid genomes from single-molecule long read sequencing. Takes as input aligned BAM/CRAM file and outputs phased VCF file with variants and haplotype information.

Proper citation: longshot (RRID:SCR_025318) Copy   

•   Source: SciCrunch Registry

https://trna.ucsc.edu/tRAX/

Software package built for in-depth analyses of tRNA-derived small RNAs (tDRs), mature tRNAs, and inference of RNA modifications from high-throughput small RNA sequencing data. Used for integrating analysis of tRNAs, tRNA-derived small RNAs, and tRNA modifications.

Proper citation: tRNA Analysis of eXpression (RRID:SCR_025486) Copy   

•   Source: SciCrunch Registry

https://github.com/willtownes/glmpca

Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data.

Proper citation: glmpca (RRID:SCR_025517) Copy   

•   Source: SciCrunch Registry

https://github.com/bmvdgeijn/WASP/

Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery.

Proper citation: WASP (RRID:SCR_025497) Copy   

•   Source: SciCrunch Registry

https://pepatac.databio.org/en/latest/

Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats.

Proper citation: PEPATAC (RRID:SCR_024758) Copy   

•   Source: SciCrunch Registry

https://jackbibby1.github.io/SCPA/

Software R package for pathway analysis in scRNA-seq data. It’s a different approach to pathway analysis that defines pathway activity as a change in multivariate distribution of a given pathway across conditions, rather than enrichment or over representation of genes.

Proper citation: Single Cell Pathway Analysis (RRID:SCR_024909) Copy   

•   Source: SciCrunch Registry