cassj/ProjectManager

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Created over 13 years ago
Updated over 13 years ago

cassj/ProjectManager

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Tools for keeping track of bioinfo projects

brat-docker

containerised brat (http://brat.nlplab.org/)

awesomething

playing with the sciverse stuff at dev8D

my_bioinfo_scripts

Just a dumping ground for an assortment of bioinformatics scripts in various states of disrepair.

chipseq_pipeline

Scripts for Buckley Lab ChIPseq pipeline

primer_designer

Primer design helpers for the Buckley lab

REST_ChIP_timecourse

science_hackday_thing

biomart-docker

Containerised biomart

REST_ChIPseq_109-109

Chiara Soldati's REST ChIPseq in 109/109 cells

mef_h3k4me3_mikkelsen

H3k4me3 ChIPseq in Mouse Embryonic Fibroblasts from Mikkelsen

excel2csv

make csv files form simple excel workbooks

ns5_vs_ns5dastro_lumixpn

Manu & Angela's NS5 vs NS5-derived astrocyte Illumina Bead Array expression data

mikkelsen07

ChIPseq data from Mikkelsen '07 (|doi:10.1038/nature06008)

FloRes_vs_FloResCre_RNAseq

Chiara Soldati's RNAseq (SOLiD) data from ESC cells with a REST Conditional Knockout

ctx_bmp_lumiarray

Alessandro Michelucci's NS5/CTX BMP/FBS Illumina expression data

chiara_miRNA_REST

DNRest_aNSCvNS5

A comparison of the effects of DNRest in NS5 and aNSC

catpaws

CApistrano Tasks Pertaining to AWS

pasquale_DNRest_illumina

Pasquale's DNRest illumina expression data

neuronal_cell-line_faireseq

Gerome Breen's Neuronal Cell Line FAIREseq data

Magdalena_Astrocytes

Expression data from Goetz lab

Rest_ChIPseq_timecourse

Rest ChIPseq timecourse (Chiara Soldati)

Creyghton_H3k27ac

Histone H3K27ac separates active from poised enhancers and predicts developmental state

DNREST_expression_mouse_astrocyte_volta

Illumina expression arrays, DN-REST v Empty Vector in mouse Astrocytes, Manuela Volta

bithell_Mash1_ChIP_meta

Abrajano_REST_CoREST_ChIPchip_stemcells

doi:10.1371/journal.pone.0007936

Abrajano_REST_CoREST_ChIPchip_neuronal

doi:10.1371/journal.pone.0007936

role_of_rest_in_astrocytes

Integrative analysis of various REST in astrocyte datasets

Abrajano_REST_CoREST_ChIPchip_glial

doi:10.1371/journal.pone.0007665

puppet_stuff

bioperl-sfold

Bioperl Run wrappers for Sfold

ns5_h3k4me3_chipseq

Alessandro's H3k4me3 ChIPseq data from NS5

dzil-profiles

piman

bioperl-unafold

Bioperl wrapper, parser for Unafold

cahoy_et_al

motifieR

Classes and functions for creating, manipulating and using PSSMs in R

ns5dastro_h34kme3_chipseq

Alessandro's H3k4me3 ChIPseq data from NS5-derived Astrocytes

FloResCre_ChIPseq

ChIPseq for various Histone modifications in FloRes and FloResCre cell lines (Chiara Soldati)

mouse_ESC_REST_ChIPseq

mohn_08_chipchip

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

rome

R-Omics Made Easy: Framework for easy generation of R-based web interfaces and workflows

volta_REST_ChIP_meta

ns5_ns5dastro_h3k4me3_peakdiff

aSVZ_REST_ChIP

CTX12_H3K4me4_ChIPseq_mini

CTX12_Astro_H3K4me_ChIPseq

Alessandro Michelucci's ChIPseq for H3K4me3 (vs Input) in CTX12 NSCs and in Astrocytes derived from that cell line

DNRest_timecourse_lumixpn

Expression data from DNRest Time Course (Chiara Soldati)

SVMergeSGE

modifications to SVMerge to generate SGE jobs instead of LSF

bioperl-wrapperbase-accessors

Autogeneration of accessors for parameters in bioperl wrappers

Johnson_CHIPPET

Rory Johnson's REST ChIPPET and expression data from ESC and NS5 cells

buckley_ami

mouse_NSC_REST_ChIP

Chiara_d4_c18_timecourse_expression

REST_ChIP_mouse_astrocytes_volta

Manuela Volta's REST ChIP in Astrocytes