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c.elegans.spatial.transcriptomics

Analysis scripts for the Ebbing et manuscript: "Spatially-resolved transcriptomics in C. elegans identifies sex-specific differences in gene expression patterns"

caars

CAARS: Comparative Assembly and Annotation of RNA-Seq data

cafe_fig

A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)

camsa

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

canthatch

Analyses, data, and scripts to identifying the wheat stem rust suppressor gene in wheat cv. Canthatch

cattlesexchromosomesassembly

cd_rf_microbiome

Scripts for processing and analyzing the microbiome data associated with the manuscript "Multi-omics Differentially Classify Disease State and Treatment Outcome in Paediatric Crohn’s Disease"

cdna_cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

celligner_ms

Code related to the Celligner manuscript

centroflye

An algorithm for centromere assembly using long error-prone reads

centromere_seeker

bash script to search for centromeric repeat patterns in PacBio data, using several current tools (trf and R)

chain_filter

chromosome-quotient

Pipeline to identify interesting Y chromosome genes

circle_dna

circos-pipeline

circos pipeline

circpseudo

Pipeline for circRNA-derived pseudogenes

circtools

circtools: a modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.

cisase

cisASE: A likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data

clustering_homologs

clustersploter

visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in Chrome by click the feature, fragments genome view

cnvrepeat

code4cos

coimbra-et-al-2021_currbiol

Code used to analyse WGS data of giraffe in Coimbra et al. 2021 (https://doi.org/10.1016/j.cub.2021.04.033)

combine2contigs

comparative-transcriptome-analysis

Analysis of RNA-Seq data accompanying the project titled 'Comparative transcriptome profiling of human and pig intestinal epithelial cells after porcine delta coronavirus infection'

comparetranscriptome

repository of scripts for comparative transcriptome analysis

convphy

cookbook

core-genome-alignment

Scripts to analyze gene content and make a concatenated alignment of core genes from bacterial genomes.

corset

Software for clustering de novo assembled transcripts and counting overlapping reads