ecosyste.ms

Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.

Papers: 10.1186/s13058-021-01451-6

https://doi.org/10.1186/s13058-021-01451-6

Transcriptome and genome evolution during HER2-amplified breast neoplasia

Cited by: 3
Author(s): Peipei Lu, Joseph W. Foley, Chunfang Zhu, Katherine McNamara, Korsuk Sirinukunwattana, Sujay Vennam, Sushama Varma, Hamid Fehri, Arunima Srivastava, Shirley Zhu, Jens Rittscher, Parag Mallick, Christina Curtis, Robert B. West
Published: about 4 years ago

Software Mentions 11

bioconductor: cellscape

Explores single cell copy number profiles in the context of a single cell tree
Papers that mentioned: 1

Very Likely Science (90)

bioconductor: copynumber

Segmentation of single- and multi-track copy number data by penalized least squares regression.
Papers that mentioned: 13

Very Likely Science (100)

bioconductor: DESeq2

Differential gene expression analysis based on the negative binomial distribution
Papers that mentioned: 9,583

Very Likely Science (100)

bioconductor: limma

Linear Models for Microarray Data
Papers that mentioned: 7,776

Very Likely Science (78)

bioconductor: QDNAseq

Quantitative DNA Sequencing for Chromosomal Aberrations
Papers that mentioned: 31

Very Likely Science (100)

bioconductor: singscore

Rank-based single-sample gene set scoring method
Papers that mentioned: 13

Very Likely Science (100)

cran: lme4

Linear Mixed-Effects Models using 'Eigen' and S4
Papers that mentioned: 9,267

Very Likely Science (100)

cran: phangorn

Phylogenetic Reconstruction and Analysis
Papers that mentioned: 192

Very Likely Science (100)

cran: STAR

Spike Train Analysis with R
Papers that mentioned: 5,759

Very Likely Science (100)

pypi: CNVkit

Copy number variation toolkit for high-throughput sequencing.
Papers that mentioned: 161

Very Likely Science (65)

pypi: picard

The next generation MusicBrainz tagger
Papers that mentioned: 243

Very Likely Science (65)