A Guide to Free and Open-Source Tools for Flow Cytometry, Gene Expression, and Genomics

October 10, 2024 Off By admin

This list offers a variety of tools across different categories related to Flow Cytometry, Gel Electrophoresis, Gene Expression Microarray, Gene Suppression, Genomics, and High-throughput Sequencing. Each tool is categorized based on its functionality, with notes on whether it’s free or available with a free trial. These tools cover important aspects like data analysis, clustering, fluorescence detection, gene expression evaluation, RNAi toolkits, genome annotation, and sequence alignment. Each entry provides a brief description to help you select the appropriate software for your research needs.

Table of Contents

Tools for Flow Cytometry

Software / Tool	Category	Free	FreeTrial	Tool Description	Link
FlowUtils	Flow Cytometry	yes		FlowUtils provides a package with utilities for flow cytometry data.	Link
FlowQB	Flow Cytometry	yes		FlowQB is a fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.	Link
fluorescence-minus-one controls	Flow Cytometry	yes		Based on comparison to fluorescence-minus-one the semi-automated algorithm helps in population discovery. Thus transferring the problem into that of one-class classification, as opposed to being an unsupervised learning problem.	Link
immunoClust	Flow Cytometry	yes		ImmunoClust is an automated analysis pipeline for uncompensated fluorescence and mass cytometry data, which consists of two parts. First, cell events of each sample are grouped into individual clusters. Subsequently, a classification algorithm assorts these cell event clusters into populations comparable between different samples. The clustering of cell events is designed for datasets with large event counts in high dimensions as a global unsupervised method, sensitive to identify rare cell types even when next to large populations.	Link
ViSNE	Flow Cytometry	yes		ViSNE allows one to map high-dimensional cytometry data onto two dimensions, yet conserve the high-dimensional structure of the data.	Link
Fluorescence Spectra Analyzer	Flow Cytometry	yes		BioLegend’s Fluorescence Spectra Analyzer is useful for the analysis of excitation and emission spectra of commonly used fluorochromes for flow cytometry.	Link
FlowJo	Flow Cytometry		yes	FlowJo is an analysis platform for single-cell flow and mass cytometry analysis. FlowJo provides an intuitive interface, specialized analysis platforms, and open-ended plugin architecture. FlowJo supports your statistical work e.g in immunophenotyping, cell cycle, proliferation, kinetics studies, quantitative population comparison, or plate screening assays.	Link
FCS Express 6	Flow Cytometry		yes	FCS Express 6 Flow Cytometry and Image Cytometry Software can turn your flow cytometry, image cytometry, and FACS data analysis into results. FCS Express supports you with plots, gates, cell cycle analysis and proliferation analysis. The data can be easily exported to microsoft office.	Link

Tools for Gel Electrophoresis

Software / Tool	Category	Free	FreeTrial	Tool Description	Link
GelClust	Gel Electrophoresis			GelClust processes gel electrophoresis images and generates the corresponding phylogenetic trees. Unlike the most of commercial and non-commercial related software tools, GelClust is very user-friendly and guides the user from image toward dendrogram through seven simple steps.	Link
Lablmage 1D	Gel Electrophoresis	yes		A flexible solution with strong image analysis algorithms is provided by Lablmage 1D. The program works for DNA or protein analysis as well as western blotting techniques. Due to its workflow-based concept, this application has become a prime example of software usability	Link
Melanie	Gel Electrophoresis		yes	Melanie provides a flexible interface to visualize, explore and analyze 2D electrophoresis gel images, in order to identify protein markers of interest through differential expression analysis.	Link

Tools for Gene Expression Microarray

Software / Tool	Category	Free	FreeTrial	Tool Description	Link
R.S. WebTool	Gene Expression Microarry	yes		R.S. WebTool is a user-friendly platform for Monte Carlo-based significance evaluation of pairwise distances.	Link

Tools for Gene Suppression

Software / Tool	Category	Free	Tool Description	Link
siRNA at Whitehead	Gene Suppression	yes	This site helps you select siRNAs to knock down your gene of interest. Enter your sequence, choose a pattern for your oligo nucleotides, and Whitehead will present you with a list of oligos matching your criteria. From this list, select those oligos you would like to consider further. All the selected oligos will be BLASTed against RefSeq, UniGene, or Ensembl database. In the BLAST result page, siRNAs can be further filtered to reduce the non-specific target effects.	Link
Lentivectors Toolbox	Gene Suppression	yes	The Lentivcetors Toolbox gives you information about Lentivectors and protocols for production and titration (ELISA / FACS).	Link
Gene Link shRNA design	Gene Suppression	yes	Gene Link shRNA design is a flexible design tool for siRNA and shRNA with custom loop sequence and cloning sites.	Link
Scramble siRNA	Gene Suppression	yes	Scramble siRNA generates a negative control for siRNA. It accepts a short DNA sequence, and returns a scrambled sequence.	Link
ShRNA Tools for RNAi	Gene Suppression	yes	ShRNA Tools for RNAi assists in the selection of empty vectors for cloning in shRNAs.	Link

Tools for Genomics

Software / Tool	Category	Free	FreeTrial	Tool Description	Link
LOVD 3.0	Genomics	yes		Free tool for Gene-centered collection and display of DNA variations.	Link
SpliceCenter	Genomics	yes		The tools on SpliceCenter help evaluating the impact of gene splicing variation on specific molecular biology techniques.	Link
GIGA	Genomics	yes		GIGA is an efficient tree building program. It supports phylogenetic reconstruction of very large gene families and determination of orthologs on a large scale.	Link
Phred	Genomics		yes	Phred is a base-calling program for DNA sequence traces. Phred it analyzes the peaks of DNA sequence chromatogram files to call bases, assigning quality scores (“Phred scores”) to each base call.	Link
CodonCode Aligner	Genomics		yes	CodonCode Aligner is a program for sequence assembly, contig editing, and mutation detection.	Link
DIALIGN	Genomics			DIALIGN aligns multiple sequence with optional user-defined constraints.	Link
Off-Spotter	Genomics	yes		Off spotter helps in the design of optimal “guide” RNAs (gRNAs) by providing several protospacer adjacent motif (PAM) choices, a run-time definition of the seed and of the allowed number of mismatches.	Link
CrispRVariants	Genomics	yes		CrispRVariants resolves and localizes individual mutant alleles with respect to the endonuclease cut site. Individual variant alleles from either traditional Sanger sequencing or high-throughput CRISPR-Cas9 mutagenesis sequencing experiments can be quantified and visualized. CrispRVariants allows users to detect problems and filter sequences appropriately before estimating mutation efficiency. This toolkit can be easily used to create a variant allele summary plot and accompanying table of counts. CrispRVariants enables immediate comparison of variant spectra between target locations.	Link
CRISPOR	Genomics	yes		CRISPOR assists with guide selection in 120 genomes, including plants and many emerging model organisms, and pre-calculated results for all human coding exons as a UCSC Genome Browser track. Enhanced off-target prediction accuracy.	Link
Breaking CAS	Genomics	yes		Breaking CAS is a versatile system for detecting putative sgRNA off-targets in CRISPR/Cas applications. BreakingCas allows working with all eukaryotic genomes available in the ENSEMBL database, for a detailed inspection of the genomic neighbourhood of every single potential off-target so as to qualitatively assess them. This web server allows specifying the characteristics and parameters of the nuclease to be used, although predefined set are available for several popular Cas proteins.	Link
BioGPS	Genomics	yes		BioGPS serves as a customizable gene annotation portal, with information about gene and protein function	Link
Genome Browser	Genomics	yes		With the Genome Browser you are able to interactively visualize genomic data. Choose between a variety of spezies and search for a specifc section to get detailled information	Link

Tools for High-throughput Sequencing

Software / Tool	Category	Free	FreeTrial	Tool Description	Link
SAMtools	High-throughput Sequencing	yes		SAMtools is a suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting SAM/BAM/CRAM format. Another feature is to index reference sequence in the FASTA format or extract subsequence from indexed reference sequence.	Link
CRISPR-AnalyzeR for pooled screens caRpools	High-throughput Sequencing	yes		CaRpools is an R package for exploratory data analysis providing CRISPR/Cas9 screen analysis. CaRpools integrates screening documentation and generation of standardized analysis reports. Its open virtual appliance allows analysis without prior programming knowledge and is therefore suited for novice and expert users.	Link
Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout MAGeCK	High-throughput Sequencing	yes		MAGeCK identifies positively and negatively selected sgRNAs and genes in genome-scale CRISPR/Cas9 knockout experiments. The workflow can be partitioned into four steps: read count normalization, mean-variance modeling, sgRNA ranking and gene ranking. MAGeCK outperforms existing computational methods in its control of the false discovery rate (FDR) and its high sensitivity.	Link
ScreenBEAM	High-throughput Sequencing	yes		Screening Bayesian Evaluation and Analysis Method (ScreenBEAM) is an R package to do gene-level meta-anlaysis of high-throughput functional genomics RNAi or CRISPR screening data.	Link
HiTSelect	High-throughput Sequencing	yes		A comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene silencing efficiency and sequencing depth of coverage and integrating relevant metadata. HiTSelect is implemented as an open-source package, with a user-friendly interface for data visualization and pathway exploration.	Link
CRISPRs	High-throughput Sequencing	yes		CRISPRs enables the detection of CRISPRs in locally-produced data and consultation of CRISPRs present in the database. If CRISPR-associated (cas) genes are annotated the program will show them as well.	Link
EBARDenovo	High-throughput Sequencing	yes		EBARDenovo is a highly accurate de novo assembly of RNA-Seq with efficient chimera-detection.	Link
Blast2GO	High-throughput Sequencing	yes		Blast2GO is spepcialized for annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. With the help of an algorithm that considers similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations Blast2GO optimizes function transfer from homologous sequences. The tool includes numerous functions for the visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim.	Link
CodingQuarry	High-throughput Sequencing	yes		CodingQuarry is a highly accurate, self-training GHMM fungal gene predictor designed to work with assembled, aligned RNA-seq transcripts. Predictions are made directly from transcript sequences which is possible through the high quality of fungal transcript assemblies. Correct predictions are made despite transcript assembly problems, including those caused by overlap between the transcripts of adjacent gene loci.	Link
HOMER	High-throughput Sequencing	yes		HOMER consists out of suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.	Link
NGS-QC	High-throughput Sequencing	yes		NGS-QC (Next Generation Sequencing Quality Control Generator) is a computational-based approach that infers quality indicators from the distribution of sequenced reads associated to a particular NGS profile.	Link
kmerHMM	High-throughput Sequencing	yes		KmerHMM is suited for Motif Discovery on Protein Binding Microarray (PBM) data using Hidden Markov Model and Belief Propagation.	Link
CexoR	High-throughput Sequencing	yes		CexoR enables strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package ‘idr’.	Link
HATSEQ	High-throughput Sequencing	yes		HATSEQ identifies functional regions of interest (ROIs) on the genome where a genomic signal significantly deviates from the general genome-wide behavior. The program provides different visualizations and statistical summaries for the detected ROIs and includes a number of built-in post-analyses with which biological meaning can be attached to the detected ROIs in terms of gene pathways and de-novo motif analysis. No further knowledge of scripting languages required.	Link
plasmidSPAdes	High-throughput Sequencing	yes		PlasmidSPAdes assembles plasmids from whole genome sequencing data. It utilizes SPAdes for transforming the de Bruijn graph into the assembly graph and finds a subgraph of the assembly graph that we refer to as the plasmid graph. It further uses ExSPAnder for repeat resolution in the plasmid graph using paired reads and generates plasmidic contigs.	Link
PlasmidFinder 1.3	High-throughput Sequencing	yes		PlasmidFinder 1.3 identifies plasmids in total or partial sequenced isolates of bacteria. PlasmidFinder can be used for replicon sequence analysis of raw, contig group, or completely assembled and closed plasmid sequencing data. The current database consists of 116 replicon sequences that match with at least at 80% nucleotide identity all replicon sequences identified in the 559 fully sequenced plasmids. The program detects a broad variety of plasmids that are often associated with antimicrobial resistance in clinically relevant bacterial pathogens.	Link
OrfM	High-throughput Sequencing	yes		OrfM rapidly identifies open reading frames (ORFs) in sequence data by applying the Aho-Corasick algorithm to find regions uninterrupted by stop codons. Ist up to five times faster than comparable tools like ‘GetOrf’ and ‘Translate’. While OrfM is sequencing platform-agnostic, it is best suited to large, high quality datasets such as those produced by Illumina sequencers.	Link
IGV	High-throughput Sequencing	yes		The Integrative Genomics Viewer (IGV) can be used to explore large integrated genomic datasets and visualize them. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.	Link
FastQC	High-throughput Sequencing	yes		A quality control tool for high throughput sequence data.	Link
Picard	High-throughput Sequencing	yes		A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.	Link
CLC Workbench	High-throughput Sequencing		yes	The CLC Workbench combines many useful features for DNA, RNA, and protein sequence data analysis. The features include: Editor for graphically and algorithmically advanced primer design/ Assembly of DNA sequence data/ Molecular cloning /Advanced RNA structure prediction and editing/ Integrated and advanced gene expression analysis /Integrated 3D molecule view