NEST package

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NEST is available under the GNU Public License Version 3. It has been tested on Linux and Mac OS X.

sample data

You can download sample networks and expression profiles and try out some analysis.

STRING networks: All networks are processed from STRING database v9 for model organisms. All confidence scores stay within range (0,1].
H.sapiens (Human): named with Entrez gene IDs
M.musculus (Mouse): named with Entrez gene IDs
D.melanogaster (Fly): named with Flybase CG IDs
C.elegans (Worm): named with Wormbase gene IDs
S.cerevisiae (Yeast): name with SGD systematic names

ENCODE cell line expression: Gene expression from ENCODE Exon Array. The values for each gene are mean-centered. Column names are cell lines. Row names are Entrez gene IDs.
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CRISPR screen in K562: The CRISPR screen data is directly downloaded from a study of Gilbert and colleagues. Column names are screen conditions. Row names are Entrez gene IDs.
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CRISPR screen in HL60 and KBM7: The CRISPR screen data is directly downloaded from a study of Wang and colleagues. Column names are cell lines. Row names are Entrez gene IDs.
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Essential and non-essential gene list: MAGECK 5.0 is used to call these gene list, used for ROC analysis in our paper. Entrez Gene ID is used and gene names are separated by ",".
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