Grid Cell Counter is a freeware biology tool that will help you to manually count the cells shown on computer screen by displaying a transparent or semi-transparent grid over your image.
Cell Counter is for counting cells (or other things). There is a choice for 4, 8, 12, 16 counters. Different (default) alarms and names. There is also a total sum with alarm. Custom settings, copy to Excel, etc..
This software is free to anyone, just for fun send author a postcard: AMC, Cell biology & Histology CMO, Ron Hoebe, Room M3-106-1
Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
TCC provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES).
Plasmodium Autocount automatically identify red blood cells and red blood cells infected with Plasmodium in a set of images. The software identifies cells using a circlular Hough transform, then looks for stained spots within cells as evidence of infection. Identified cells that are misshapen (debris on the slide) or have too much stain (white blood cells) are discarded.
tweeDEseq is an R package for analyzing RNAseq count data. It implements Poisson-Tweedie family of distributions to model count data distribution. This family includes Poisson and Negative Bionomial as particular cases. The testPT test is used to detect genes that are differentially expressed (DE).
Count is a software package for the evolutionary analysis of homolog family sizes (phylogenetic profiles), or other numerical census-type characters along a phylogeny. The principal data consist of the distribution of homolog family sizes across multiple genomes: for each (gene) family, that table gives the number of homologs identified in each genome.
Breakpoint Calculator calculates pairwise and three-way hidden breakpoint counts for each pair and triplet of genomes.The breakpoint calculator constructs a weighted graph from the adjacencies of the genomes in the alignment and computes a maximum weight perfect matching.
OligoCounter is a Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. These oligos can be useful in visualising small genomes on a global basis (see figure below), investigating repeats at certain regions, and for attributing short reads (for example from metagenomics) to a sequenced genome.
OligoViz : allows direct visualisation of OligoCounter data
OligoWords : generates 4mer data for JCircleGraph (use the perl script to extract 4mer data from a fasta file).
JCircleGraph : visualisation of 4mer and OligoCounter data in attractive genome atlases (requires 4mer files from OligoWords!).