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https://github.com/cbrueffer/tophat-recondition

Software tool as post-processor for TopHat unmapped reads that restores read information in the proper format.Enables downstream software to process plethora of BAM files written by TopHat.

Proper citation: TopHat-Recondition (RRID:SCR_024383) Copy   

•   Source: SciCrunch Registry

https://www.teuniz.net/edfbrowser/

Open source, multiplatform, universal viewer, annotator and toolbox intended for time-series storage files like EEG, EMG, ECG, BioImpedance, etc.

Proper citation: EDFbrowser (RRID:SCR_024021) Copy   

•   Source: SciCrunch Registry

http://www.danielwilson.me.uk/omegaMap.html

Software tool for detecting natural selection and recombination in DNA or RNA sequences.

Proper citation: omegaMap (RRID:SCR_024143) Copy   

•   Source: SciCrunch Registry

https://www.open-emr.org/

Open source software for electronic health records and medical practice management solution.

Proper citation: OpenEMR (RRID:SCR_024144) Copy   

•   Source: SciCrunch Registry

https://github.com/nanoporetech/tombo

Software suite of tools for identification of modified nucleotides from nanopore sequencing data.Used also for analysis and visualization of raw nanopore signal.

Proper citation: Tombo (RRID:SCR_024388) Copy   

•   Source: SciCrunch Registry

http://assemblytics.com/

Web analytics tool for detection of variants from assembly. Used to detect and analyze structural variants from genome assembly by comparing it to reference genome.

Proper citation: Assemblytics (RRID:SCR_023967) Copy   

•   Source: SciCrunch Registry

https://zhanggroup.org/NW-align/

Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm.

Proper citation: NW-align (RRID:SCR_024138) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/microbegps/

Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates.

Proper citation: MicrobeGPS (RRID:SCR_024112) Copy   

•   Source: SciCrunch Registry

https://pyscanfcs.readthedocs.io/en/stable/

Software application for perpendicular line scanning fluorescence correlation spectroscopy.

Proper citation: pyscanfcs (RRID:SCR_024190) Copy   

•   Source: SciCrunch Registry

https://github.com/pyranges/pyranges

Software application for efficient comparison of genomic intervals in Python.

Proper citation: pyranges (RRID:SCR_024191) Copy   

•   Source: SciCrunch Registry

http://gmod.org/wiki/Chado

Relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals.

Proper citation: Chado (RRID:SCR_024073) Copy   

•   Source: SciCrunch Registry

https://lcb.infotech.monash.edu/mustang/

Software tool for structural alignment of multiple protein structures. Used to produce sequence alignment. Reports multiple sequence alignment and corresponding superposition of structures.

Proper citation: Mustang (RRID:SCR_024126) Copy   

•   Source: SciCrunch Registry

http://edwards.sdsu.edu/cgi-bin/prinseq/prinseq.cgi

A publicly available tool that is able to filter, reformat and trim your genomic and metagenomic sequence data and provide you summary statistics for your sequence data. The interactive web interface facilitates visualizations of the results and export functionality for subsequent data processing. The standalone lite version is written in Perl and does not require any non-core Perl modules. The lite version is primarily designed for data preprocessing and does not generate summary statistics in graphical form., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PRINSEQ (RRID:SCR_005454) Copy   

•   Source: SciCrunch Registry

http://www.tmanavigator.org/

A free web-based service open to all users for analysis of tissue microarray (TMA) data and related information, accommodating categorical, semi-continuous and continuous expression scores. There is no login requirement.

Proper citation: TMA Navigator (RRID:SCR_005599) Copy   

•   Source: SciCrunch Registry

http://www.neuroepigenomics.org/methylomedb/

A database containing genome-wide brain DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples. Two species were included in the Brain Methylome Database: human and mouse. Human postmortem brain samples were obtained from three distinct cortical regions, i.e., dorsal lateral prefrontal cortex (dlPFC), ventral prefrontal cortex (vPFC), and auditory cortex (AC). Human samples were selected from our postmortem brain collection with extensive neuropathological and psychopathological data, as well as brain toxicology reports. The Department of Psychiatry of Columbia University and the New York State Psychiatric Institute have assembled this brain collection, where a validated psychological autopsy method is used to generate Axis I and II DSM IV diagnoses and data are obtained on developmental history, history of psychiatric illness and treatment, and family history for each subject. The mouse sample (strain 129S6/SvEv) DNA was collected from the entire left cerebral hemisphere. The three human brain regions were selected because they have been implicated in the neuropathology of depression and schizophrenia. Within each cortical region, both disease and non-psychiatric samples have been profiled (matching subjects by age and sex in each group). Such careful matching of subjects allows one to perform a wide range of queries with the ability to characterize methylation features in non-psychiatric controls, as well as detect differentially methylated domains or features between disease and non-psychiatric samples. A total of 14 non-psychiatric, 9 schizophrenic, and 6 depression methylation profiles are included in the database.

Proper citation: MethylomeDB (RRID:SCR_005583) Copy   

•   Source: SciCrunch Registry

http://llama.mshri.on.ca/funcassociate/

A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool

Proper citation: FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) Copy   

•   Source: SciCrunch Registry

http://bioinfo.iitk.ac.in/MIPModDB/

This is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins. The nearly completed sets of MIPs have been identified from the completed genome sequence of organisms available at NCBI. The structural models of MIP proteins were created by defined protocol. The database aims to provide key information of MIPs in particular based on sequence as well as structures. This will further help to decipher the function of uncharacterized MIPs. For each MIP entry, this database contains information about the source, gene structure, sequence features, substitutions in the conserved NPA motifs, structural model, the residues forming the selectivity filter and channel radius profile. For selected set of MIPs, it is possible to derive structure-based sequence alignment and evolutionary relationship. Sequences and structures of selected MIPs can be downloaded from MIPModDB database.

Proper citation: MIPModDB (RRID:SCR_006058) Copy   

•   Source: SciCrunch Registry

http://wego.genomics.org.cn/cgi-bin/wego/index.pl

Web Gene Ontology Annotation Plot (WEGO) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. Platform: Online tool

Proper citation: WEGO - Web Gene Ontology Annotation Plot (RRID:SCR_005827) Copy   

•   Source: SciCrunch Registry

http://recountdb.cbrc.jp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database for corrected read counts and genome mapping on NCBI's Short Read Archive. The corrected count was done using RECOUNT and the mapping with LAST. We also provide information of reference genome to which we aligned the short reads. We focus on transcriptomic data, specifically TSS-Seq and RNA-Seq. Because this is the type of data for which sequence count correction is most important. Hence we do not include the genomic reads. The current version contains 2,265 entries from 45 organisms, with read lengths from 17 to 100bp. Via a searchable and browseable interface users can obtain corrected data in formats useful for transcriptomic analysis. We provide the data grouped according to the genome, type of studies and submitter in TAB , PSL and BAM format. They contain the mapping position and annotation of reads observed and corrected counts.

Proper citation: RecountDB (RRID:SCR_006117) Copy   

•   Source: SciCrunch Registry

http://snps-and-go.biocomp.unibo.it/snps-and-go/

A server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans.

Proper citation: SNPsandGO (RRID:SCR_005788) Copy   

•   Source: SciCrunch Registry