pypi: utils | Projects | Ecosyste.ms: Papers

10.1186/s13104-019-4179-2

TCC-GUI: a Shiny-based application for differential expression analysis of RNA-Seq count data
Cited by: 75
Author(s): Wei Su, Jianqiang Sun, Kentaro Shimizu, Koji Kadota
Software Mentions: 20
Published: almost 6 years ago

10.12688/gatesopenres.12832.2

DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis
Cited by: 7
Author(s): Greg Finak, Bryan T. Mayer, William J. Fulp, Paul Obrecht, Alicia Sato, Eva Yin-han Chung, Drienna Holman, Raphaël Gottardo
Software Mentions: 19
Published: over 6 years ago

10.15252/msb.20209438

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics
Cited by: 49
Author(s): Carmen Bravo González-Blas, Xiao‐Jiang Quan, Ramon Duran-Romaña, Ibrahim Ihsan Taskiran, Duygu Koldere, Kristofer Davie, Valerie Christiaens, Samira Makhzami, Gert Hulselmans, Maxime De Waegeneer, David Mauduit, Suresh Poovathingal, Sara Aibar, Stein Aerts
Software Mentions: 19
Published: over 4 years ago

10.1186/s12859-019-3059-z

HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data
Cited by: 28
Author(s): Anh Tran, Alex M. Dussaq, Timothy Kennell, Christopher D. Willey, Anita B. Hjelmeland
Software Mentions: 18
Published: over 5 years ago

10.1186/s12864-021-07370-2

GCSscore: an R package for differential gene expression analysis in Affymetrix/Thermo-Fisher whole transcriptome microarrays
Cited by: 3
Author(s): Guy M. Harris, Shahroze Abbas, Michael F. Miles
Software Mentions: 17
Published: almost 4 years ago

10.1371/journal.pone.0188955

Gbm.auto: A software tool to simplify spatial modelling and Marine Protected Area planning
Cited by: 19
Author(s): Simon Dedman, Rick Officer, Maurice Clarke, David G. Reid, Deirdre Brophy
Software Mentions: 15
Published: about 7 years ago

10.1099/mgen.0.000225

Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny
Cited by: 20
Author(s): Cameron J. Reid, Matthew Z. DeMaere, Steven P. Djordjevic
Software Mentions: 14
Published: almost 6 years ago

10.3389/fvets.2019.00406

An Epidemiological and Economic Simulation Model to Evaluate Strategies for the Control of Bovine Virus Diarrhea in Germany
Cited by: 17
Author(s): Jörn Gethmann, Carolina Probst, Jason Bassett, Pascal Blunk, Philipp Hövel, Franz Josef Conraths
Software Mentions: 13
Published: about 5 years ago

10.3389/fnins.2020.00919

HYGRIP: Full-Stack Characterization of Neurobehavioral Signals (fNIRS, EEG, EMG, Force, and Breathing) During a Bimanual Grip Force Control Task
Cited by: 10
Author(s): Pablo Ortega, Tong Zhao, A. Aldo Faisal
Software Mentions: 11
Published: about 4 years ago

10.3897/BDJ.9.e71378

Molecular Acquisition, Cleaning and Evaluation in R (MACER) - A tool to assemble molecular marker datasets from BOLD and GenBank
Cited by: 2
Author(s): Reginald H.F. Young, Rekkab Gill, Daniel Gillis, Robert Hanner
Software Mentions: 11
Published: over 3 years ago

10.3390/cancers11081104

Differential Expression of DNA Repair Genes in Prognostically-Favorable versus Unfavorable Uveal Melanoma
Cited by: 10
Author(s): Mehmet Doğrusöz, Andrea Ruschel Träsel, Jinfeng Cao, Selҫuk Ҫolak, Sake I. van Pelt, Wilma G. M. Kroes, Amina F.A.S. Teunisse, Samar Alsafadi, Sjoerd G. van Duinen, Gregorius P M Luyten, Pieter A. van der Velden, Adriana Amaro, Ulrich Pfeffer, Aart G. Jochemsen, Martine J. Jager
Software Mentions: 11
Published: over 5 years ago

10.1186/s13059-018-1432-2

FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map
Cited by: 57
Author(s): Tom Aharon Hait, David Amar, Ron Shamir, Ran Elkon
Software Mentions: 10
Published: over 6 years ago

10.3389/fonc.2020.526577

Patient Stratification of Clear Cell Renal Cell Carcinoma Using the Global Transcription Factor Activity Landscape Derived From RNA-Seq Data
Cited by: 7
Author(s): Yanyan Zhu, Shundong Cang, Bowang Chen, Ye Gu, Miaomiao Jiang, Junya Yan, Fengmin Shao, Xiaoyun Huang
Software Mentions: 10
Published: about 4 years ago

10.15252/msb.20199389

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference
Cited by: 63
Author(s): Yingxin Lin, Yue Cao, Hani Jieun Kim, Agus Salim, T. P. Speed, David M. Lin, Pengyi Yang, Jean Yee Hwa Yang
Software Mentions: 9
Published: over 4 years ago

10.1371/journal.pone.0084227

Automatic Context-Specific Subnetwork Discovery from Large Interaction Networks
Cited by: 10
Author(s): Ashis Saha, Aik Choon Tan, Jaewoo Kang
Software Mentions: 9
Published: almost 11 years ago

10.1371/journal.pone.0164292

Upregulation of HLA Expression in Primary Uveal Melanoma by Infiltrating Leukocytes
Cited by: 55
Author(s): T. Huibertus van Essen, Sake I. van Pelt, Inge H. G. Bronkhorst, Mieke Versluis, Fariba Némati, Cécile Laurent, Gregorius P M Luyten, Thorbald van Hall, Peter J. van den Elsen, Pieter A. van der Velden, Didier Decaudin, Martine J. Jager
Software Mentions: 8
Published: about 8 years ago

10.1371/journal.pone.0223010

KETOS: Clinical decision support and machine learning as a service – A training and deployment platform based on Docker, OMOP-CDM, and FHIR Web Services
Cited by: 27
Author(s): Julian Gruendner, Thorsten Schwachhofer, Phillip Sippl, Nicolas Wolf, Marcel Erpenbeck, Christian Gülden, Lorenz A. Kapsner, Jakob Zierk, Sebastian Mate, Michael Stürzl, Roland S. Croner, Hans‐Ulrich Prokosch, Dennis Toddenroth
Software Mentions: 7
Published: about 5 years ago

10.7717/peerj.4320

Linking pangenomes and metagenomes: the <i>Prochlorococcus</i> metapangenome
Cited by: 272
Author(s): Tom O. Delmont, A. Murat Eren
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pone.0240041

Towards an open and decentralized case law curation ecosystem
Cited by: 1
Author(s): Eleni Panagou, Manolis Vavalis
Software Mentions: 6
Published: about 4 years ago

10.7717/peerj.1319

Anvi’o: an advanced analysis and visualization platform for ‘omics data
Cited by: 1,274
Author(s): A. Murat Eren, Özcan C. Esen, Christopher Quince, Joseph H. Vineis, Hilary G. Morrison, Mitchell L. Sogin, Tom O. Delmont
Software Mentions: 5
Published: about 9 years ago

10.3390/s21134323

Real-Time Human Recognition at Night via Integrated Face and Gait Recognition Technologies
Cited by: 15
Author(s): Samah A. F. Manssor, Shanhui Sun, Mohammed A. M. Elhassan
Software Mentions: 4
Published: over 3 years ago

10.1186/s12864-021-07696-x

kataegis: an R package for identification and visualization of the genomic localized hypermutation regions using high-throughput sequencing
Cited by: 6
Author(s): Xue Lü, Yingying Hua, Shuanglin Gu, Lili Lv, Xingyu Li, Pin Chen, Peng Dai, Yunyun Hu, Anna Liu, Jian Li
Software Mentions: 3
Published: over 3 years ago

10.1186/s13059-019-1670-y

Alevin efficiently estimates accurate gene abundances from dscRNA-seq data
Cited by: 167
Author(s): Avi Srivastava, Laraib Malik, Tom Smith, Ian Sudbery, Rob Patro
Software Mentions: 2
Published: over 5 years ago

10.1111/gcbb.12309

Genotypic diversity effects on biomass production in native perennial bioenergy cropping systems
Cited by: 19
Author(s): Geoffrey P. Morris, Zhenbin Hu, Paul Grabowski, Justin O. Borevitz, Marie‐Anne de Graaff, R. M. Miller, Julie D. Jastrow
Software Mentions: 2
Published: almost 9 years ago

10.1016/j.isci.2021.102538

Artificial neural network trained on smartphone behavior can trace epileptiform activity in epilepsy
Cited by: 8
Author(s): Robert B. Duckrow, Enea Ceolini, Hitten P. Zaveri, Cornell Brooks, Arko Ghosh
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-015-0609-x

Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature
Cited by: 24
Author(s): K. E. Ravikumar, Kavishwar B. Wagholikar, Dingcheng Li, Jean Pierre A. Kocher, Hongfang Liu
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0231222

Donor-derived IL-17A and IL-17F deficiency triggers Th1 allo-responses and increases gut leakage during acute GVHD
Cited by: 0
Author(s): Ivan Odak, Alina Depkat-Jakob, Maleen Beck, Michael Jarek, Yan Yu, Ursula Seidler, Sascha David, Arnold Ganser, Reinhold Förster, Immo Prinz, Christian Koenecke
Software Mentions: 2
Published: over 4 years ago

10.1111/cmi.12659

The β‐1,3‐glucanosyltransferases (Gels) affect the structure of the rice blast fungal cell wall during appressorium‐mediated plant infection
Cited by: 41
Author(s): Marketa Samalova, Hugo Mélida, Francisco Vilaplana, Vincent Bulone, Darren M. Soanes, Nicholas J. Talbot, Sarah J. Gurr
Software Mentions: 2
Published: about 8 years ago

10.12688/f1000research.23180.2

Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive
Cited by: 8
Author(s): Matthew N. Bernstein, Ariella L. Gladstein, Khun Zaw Latt, Emily Clough, Ben Busby, Allissa Dillman
Software Mentions: 2
Published: over 4 years ago

10.1093/gigascience/giaa065

Galactic Circos: User-friendly Circos plots within the Galaxy platform
Cited by: 26
Author(s): Helena Rasche, Saskia Hiltemann
Software Mentions: 2
Published: over 4 years ago

10.1523/ENEURO.0514-19.2020

Time-to-Target Simplifies Optimal Control of Visuomotor Feedback Responses
Cited by: 14
Author(s): Justinas Česonis, David W. Franklin
Software Mentions: 1
Published: almost 5 years ago

10.1186/1472-6947-8-42

Analysis of queries sent to PubMed at the point of care: Observation of search behaviour in a medical teaching hospital
Cited by: 45
Author(s): Arjen Hoogendam, Anton F. H. Stalenhoef, P.F. de Vries Robbé, A. John P.M. Overbeke
Software Mentions: 1
Published: about 16 years ago

10.1186/1742-5581-3-10

Technology mediator: a new role for the reference librarian?
Cited by: 6
Author(s): David Howse, Paul Bracke, Samuel M. Keim
Software Mentions: 1
Published: about 18 years ago

10.3389/fnins.2021.640016

Atrophy in the Left Amygdala Predicted Drug Responses in Idiopathic Generalized Epilepsy Patients With Tonic–Clonic Seizures
Cited by: 2
Author(s): Xin Li, Zhongyuan Wang, Qian Chen, Xiaoyun Wang, Zhao Qing, Wen Zhang, Jiaming Lu, Junxia Wang, Xin Zhang, Jiani Liu, Zhengge Wang, Baoxin Li, Bing Zhang
Software Mentions: 1
Published: over 3 years ago

10.1186/s12859-018-2286-z

Dense neural networks for predicting chromatin conformation
Cited by: 13
Author(s): Pau Farré, Alexandre Heurteau, Olivier Cuvier, Eldon Emberly
Software Mentions: 1
Published: about 6 years ago

Ecosyste.ms: Papers

Projects: pypi: utils

Papers Mentioning utils 35