Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: Rsamtools
https://packages.ecosyste.ms/registries/bioconductor.org/packages/Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
2 versions
Latest release: 12 months ago
205 dependent packages
3,527,034 downloads total
Papers Mentioning Rsamtools 138
10.1186/s12864-019-6313-x
Secretory RING finger proteins function as effectors in a grapevine galling insectCited by: 13
Author(s): Chaoyang Zhao, Claude Rispe, Paul D. Nabity
Software Mentions: 3
Published: almost 5 years ago
10.1186/s12864-015-1583-4
Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiaeCited by: 44
Author(s): Isabelle Rosinski‐Chupin, Elisabeth Sauvage, Odile Sismeiro, Adrien Villain, Violette Da Cunha, Marie-Elise Caliot, Marie‐Agnès Dillies, Patrick Trieu-Cuot, Philippe Bouloc, Marie‐Frédérique Lartigue, Philippe Glaser
Software Mentions: 3
Published: over 9 years ago
10.7554/eLife.46711
Embryo polarity in moth flies and mosquitoes relies on distinct old genes with localized transcript isoformsCited by: 23
Author(s): Yoseop Yoon, Jeff Klomp, Inés Martín-Martín, Frank Criscione, Eric Calvo, José M. C. Ribeiro, Urs Schmidt‐Ott
Software Mentions: 3
Published: about 5 years ago
10.1016/j.cell.2021.03.012
Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactionsCited by: 126
Author(s): Ryan A. Flynn, Julia A. Belk, Yanyan Qi, Yuki Yasumoto, Wei Jin, Mia Madel Alfajaro, Quanming Shi, Maxwell R. Mumbach, Aditi Limaye, Peter C DeWeirdt, Cameron O. Schmitz, Kevin R. Parker, Elizabeth Woo, Howard Y. Chang, Tamás L. Horváth, Jan E. Carette, Carolyn R. Bertozzi, Craig B. Wilen, Ansuman T. Satpathy
Software Mentions: 3
Published: over 3 years ago
10.1186/1471-2148-12-94
Uninformative polymorphisms bias genome scans for signatures of selectionCited by: 131
Author(s): Marius Roesti, Walter Salzburger, Daniel Berner
Software Mentions: 3
Published: over 12 years ago
10.1371/journal.pone.0247031
Endangered predators and endangered prey: Seasonal diet of Southern Resident killer whalesCited by: 33
Author(s): M. Bradley Hanson, Candice K. Emmons, Michael J. Ford, Meredith V. Everett, Kim M. Parsons, Linda K. Park, Jennifer A. Hempelmann, Donald M. Van Doornik, Gregory S. Schorr, Jeffrey K Jacobsen, Mark F Sears, Maya S Sears, John G. Sneva, Robin W. Baird, Lynne Barrè
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-017-12084-1
DNA Methylomes Reveal Biological Networks Involved in Human Eye Development, Functions and Associated DisordersCited by: 36
Author(s): María Berdasco, Antonio Gómez, Marc Rubio, Jaume Català‐Mora, Vicente Zanón‐Moreno, Miguel López, Cristina Hernández, Shigeo Yoshida, Takahito Nakama, Keijiro Ishikawa, Tatsuro Ishibashi, Amina Boubekeur, Lotfi Louhibi, Miguel Ángel Pujana, Sergi Sayols, Fernando Setién, Dolores Corella, Carmen de Torres, Andreu Parareda, Ling Zhao, Kang Zhang, Matilde E. Lleonart, Javier Alonso, Rafael Simó, Josep M. Caminal, Manel Esteller
Software Mentions: 3
Published: about 7 years ago
10.3390/v13030437
viromeBrowser: A Shiny App for Browsing Virome Sequencing Analysis ResultsCited by: 1
Author(s): David F. Nieuwenhuijse, Bas B. Oude Munnink, Marion Koopmans
Software Mentions: 3
Published: over 3 years ago
10.3390/vaccines9060616
A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in IsraelCited by: 20
Author(s): Neta S. Zuckerman, Shay Fleishon, Efrat Bucris, Dana Bar-Ilan, Michal Linial, Itay Bar-Or, Victoria Indenbaum, Merav Weil, Yaniv Lustig, Ella Mendelson, Michal Mandelboim, Orna Mor, Neta S. Zuckerman
Software Mentions: 3
Published: over 3 years ago
10.1128/JVI.00571-17
Uncovering the Repertoire of Endogenous Flaviviral Elements in Aedes Mosquito GenomesCited by: 75
Author(s): Yasutsugu Suzuki, Lionel Frangeul, Laura B. Dickson, Hervé Blanc, Yann Verdier, Joëlle Vinh, Louis Lambrechts, Maria‐Carla Saleh
Software Mentions: 2
Published: about 7 years ago
10.1007/s00401-017-1714-x
Deleterious ABCA7 mutations and transcript rescue mechanisms in early onset Alzheimer’s diseaseCited by: 49
Author(s): Arne De Roeck, Tobi Van den Bossche, Julie van der Zee, Jan Verheijen, Wouter De Coster, Jasper Van Dongen, Lubina Dillen, Yalda Baradaran-Heravi, Bavo Heeman, Raquel Sánchez‐Valle, Albert Lladó, Benedetta Nacmias, Sandro Sorbi, Ellen Gelpí, Oriol Grau‐Rivera, Estrella Gómez‐Tortosa, Pau Pástor, Sara Ortega‐Cubero, María A. Pastor, Caroline Graff, Håkan Thonberg, Luisa Benussi, Roberta Ghidoni, Giuliano Binetti, Alexandre de Mendonça, Madalena Martins, Barbara Borroni, Alessandro Padovani, Maria Rosário Almeida, Isabel Santana, Janine Diehl‐Schmid, Panagiotis Alexopoulos, Jordi Clarimón, Alberto Lleó, Juan Fortea, Magda Tsolaki, Maria Koutroumani, Radoslav Matěj, Zdeněk Rohan, Peter De Deyn, Sebastiaan Engelborghs, Patrick Cras, Christine Van Broeckhoven, Kristel Sleegers
Software Mentions: 2
Published: over 7 years ago
10.1186/s12859-021-04060-4
Improving high-resolution copy number variation analysis from next generation sequencing using unique molecular identifiersCited by: 6
Author(s): Pierre‐Julien Viailly, Vincent Sater, Mathieu Viennot, Élodie Bohers, Nicolas Vergne, Caroline Bérard, Hélène Dauchel, Thierry Lecroq, Alison Celebi, Philippe Ruminy, Vinciane Marchand, Marie‐Delphine Lanic, Sydney Dubois, Dominique Penther, Hervé Tilly, Sylvain Mareschal, Fabrice Jardin
Software Mentions: 2
Published: over 3 years ago
10.1186/1471-2105-14-S11-S3
Efficient digest of high-throughput sequencing data in a reproducible reportCited by: 4
Author(s): Zhe Zhang, Jeremy Leipzig, Ariella Sasson, Angela M Yu, Juan C. Perín, Hongbo Xie, Mahdi Sarmady, Patrick V. Warren, Peter S. White
Software Mentions: 2
Published: about 11 years ago
10.1186/s12859-020-3508-8
Origins and characterization of variants shared between databases of somatic and germline human mutationsCited by: 10
Author(s): William Meyerson, John Leisman, Fábio C. P. Navarro, Mark Gerstein
Software Mentions: 2
Published: over 4 years ago
10.1186/s12864-020-6542-z
Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasetsCited by: 4
Author(s): Haruka Ozaki, Tetsutaro Hayashi, Mana Umeda, Itoshi Nikaido
Software Mentions: 2
Published: over 4 years ago
10.1186/s13104-015-1404-5
VING: a software for visualization of deep sequencing signalsCited by: 20
Author(s): Marc Descrimes, Yousra Ben Zouari, Maxime Wéry, Rachel Legendre, Daniel Gautheret, Antonin Morillon
Software Mentions: 2
Published: about 9 years ago
10.1093/bioinformatics/btu419
RAPIDR: an analysis package for non-invasive prenatal testing of aneuploidyCited by: 26
Author(s): Kitty Lo, C. R. Boustred, Lyn S. Chitty, Vincent Plagnol
Software Mentions: 2
Published: over 10 years ago
10.3390/v13030511
Comparative Analysis of Within-Host Mutation Patterns and Diversity of Hepatitis C Virus Subtypes 1a, 1b, and 3aCited by: 2
Author(s): Kaho H. Tisthammer, Weiyan Dong, Jeffrey B. Joy, Pleuni S. Pennings
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0029002
Deep Sequencing Whole Transcriptome Exploration of the σE Regulon in Neisseria meningitidisCited by: 25
Author(s): Robert Antonius Gerhardus Huis in ‘t Veld, Antonius Marcellinus Willemsen, A. H. C. van Kampen, Edward J. Bradley, Frank Baas, Yvonne Pannekoek, Arie van der Ende
Software Mentions: 2
Published: almost 13 years ago
10.1371/journal.pone.0229449
Proteolysis and cartilage development are activated in the synovium after surgical induction of post traumatic osteoarthritisCited by: 10
Author(s): Ugur M. Ayturk, Jakob T. Sieker, Carla M. Haslauer, Benedikt L. Proffen, Manuela Weißenberger, Matthew L. Warman, Braden C. Fleming, Martha M. Murray
Software Mentions: 2
Published: over 4 years ago
10.1371/journal.pone.0039359
Molecular Effects of Doxycycline Treatment on Pterygium as Revealed by Massive Transcriptome SequencingCited by: 20
Author(s): Ignacio M. Larráyoz, Alberto de Luis, Óscar Rúa, Sara Velilla, Juan Cabello, Alfredo Martı́nez
Software Mentions: 2
Published: over 12 years ago
10.15252/emmm.202114060
<i>rs41291957</i> controls miR‐143 and miR‐145 expression and impacts coronary artery disease riskCited by: 10
Author(s): Ignacio Fernando Hall, Montserrat Climent, Chiara Anselmi, Laura Papa, Vinicius Tragante, Luca Lambroia, Floriana Maria Farina, Marcus E. Kleber, Winfried März, Carlo Biguori, Gianluigi Condorelli, Leonardo Elia
Software Mentions: 2
Published: about 3 years ago
10.1186/s13059-015-0648-7
Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomasCited by: 37
Author(s): Anthony Mathelier, Calvin Lefebvre, Allen W. Zhang, David J. Arenillas, Jiarui Ding, Wyeth W. Wasserman, Sohrab P. Shah
Software Mentions: 2
Published: over 9 years ago
10.1186/s13059-019-1683-6
Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybeanCited by: 13
Author(s): Jinyu Wang, Xianran Li, Kyung Do Kim, Michael J. Scanlon, Scott A. Jackson, Nathan M. Springer, Jianming Yu
Software Mentions: 2
Published: over 5 years ago
10.1111/jeb.13443
How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in <i>Daphnia magna</i>Cited by: 13
Author(s): Marinela Dukič, Daniel Berner, Christoph R. Haag, Dieter Ebert
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-021-94491-z
Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western EuropeCited by: 20
Author(s): Adam B Rohrlach, Luka Papac, Ainash Childebayeva, Maïté Rivollat, Vanessa Villalba-Mouco, Gunnar U. Neumann, Sandra Penske, Eirini Skourtanioti, Marieke Sophia van de Loosdrecht, Murat Akar, Kamen Boyadzhiev, Yavor Boyadzhiev, Marie‐France Deguilloux, Miroslav Dobeš, Yılmaz Selim Erdal, Michal Ernée, Marcella Frangipane, Mirosław Furmanek, Susanne Friederich, Emmanuel Ghesquière, Agata Hałuszko, Svend Hansen, Mario Küßner, Marcello A. Mannino, Rana Özbal, Sabine Reinhold, Stéphane Rottier, Domingo C. Salazar‐García, Jorge Soler Díaz, Philipp W. Stockhammer, Consuelo Roca de Togores Muñoz, K. Aslıhan Yener, Cosimo Posth, Johannes Krause, Alexander Herbig, Wolfgang Haak
Software Mentions: 2
Published: about 3 years ago
10.1016/j.jmoldx.2018.07.005
Effects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer PatientsCited by: 75
Author(s): Bente Risberg, Dana W.Y. Tsui, Heather Biggs, Andrea Ruiz-Valdepenas Martin de Almagro, Sarah-Jane Dawson, Charlotte Hodgkin, Linda Jones, Christine Parkinson, Anna Piskorz, Francesco Marass, Dineika Chandrananda, Elizabeth Moore, James A. Morris, Vincent Plagnol, Nitzan Rosenfeld, Carlos Caldas, James D. Brenton, Davina Gale
Software Mentions: 2
Published: almost 6 years ago
10.3390/ijms160922046
Identification of Conserved and Novel MicroRNAs during Tail Regeneration in the Mexican AxolotlCited by: 15
Author(s): Micah D. Gearhart, Jami R. Erickson, Andrew Walsh, Karen Echeverri
Software Mentions: 2
Published: about 9 years ago
10.1007/s00401-018-1841-z
An intronic VNTR affects splicing of ABCA7 and increases risk of Alzheimer’s diseaseCited by: 64
Author(s): Arne De Roeck, Lena Duchateau, Jasper Van Dongen, Rita Cacace, Maria Bjerke, Tobi Van den Bossche, Patrick Cras, Rik Vandenberghe, Peter Paul De Deyn, Sebastiaan Engelborghs, Christine Van Broeckhoven, Kristel Sleegers
Software Mentions: 2
Published: over 6 years ago
10.3389/fonc.2018.00185
Expression of the Circadian Clock Gene BMAL1 Positively Correlates With Antitumor Immunity and Patient Survival in Metastatic MelanomaCited by: 53
Author(s): Leonardo Vinícius Monteiro de Assis, Gabriela Sarti Kinker, Maria Nathália Moraes, Regina Pekelmann Markus, Pedro Augusto Carlos Magno Fernandes, Ana Maria de Lauro Castrucci
Software Mentions: 1
Published: over 6 years ago
10.12688/f1000research.7453.1
Crambled: A Shiny application to enable intuitive resolution of conflicting cellularity estimatesCited by: 4
Author(s): Andy G. Lynch
Software Mentions: 1
Published: almost 9 years ago
10.1002/evl3.99
Predictable genome-wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fishCited by: 39
Author(s): Quiterie Haenel, Marius Roesti, Dario Moser, Andrew D. C. MacColl, Daniel Berner
Software Mentions: 1
Published: over 5 years ago
10.1016/j.cub.2020.06.057
Non-retroviral Endogenous Viral Element Limits Cognate Virus Replication in Aedes aegypti OvariesCited by: 75
Author(s): Yasutsugu Suzuki, Artem Baidaliuk, Pascal Miesen, Lionel Frangeul, Anna B. Crist, Sarah H. Merkling, Albin Fontaine, Sébastian Lequime, Isabelle Moltini-Conclois, Hervé Blanc, Ronald P. van Rij, Louis Lambrechts, Maria-Carla Saleh
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pcbi.1003419
Combinatorial Modeling of Chromatin Features Quantitatively Predicts DNA Replication Timing in DrosophilaCited by: 20
Author(s): Federico Comoglio, Renato Paro
Software Mentions: 1
Published: over 10 years ago
10.3390/v12040468
Differential Small RNA Responses against Co-Infecting Insect-Specific Viruses in Aedes albopictus MosquitoesCited by: 16
Author(s): Lionel Frangeul, Hervé Blanc, María-Carla Saleh, Yasutsugu Suzuki
Software Mentions: 1
Published: over 4 years ago
10.1128/mBio.01558-17
Genome-Wide Discovery of Genes Required for Capsule Production by Uropathogenic <i>Escherichia coli</i>Cited by: 39
Author(s): Kelvin G. K. Goh, Minh-Duy Phan, Brian M. Forde, Teik Min Chong, Wai‐Fong Yin, Kok‐Gan Chan, Glen C. Ulett, Matthew J. Sweet, Scott A. Beatson, Mark A. Schembri
Software Mentions: 1
Published: almost 7 years ago
10.1186/1471-2164-15-236
De novo transcriptome analysis of Hevea brasiliensistissues by RNA-seq and screening for molecular markersCited by: 70
Author(s): Leonardo Rippel Salgado, Daniela Martins Koop, Daniel Guariz Pinheiro, Ronan Rivallan, Vincent Le Guen, Marisa Fabiana Nicolás, Luiz Gonzaga Paula de Almeida, Viviani Ribeiro Rocha, Milena Mangefeste Magalhães, Alexandra Lehmkuhl Gerber, Antônio Figueira, Júlio Cézar De Mattos Cascardo, Ana Tereza Ribeiro de Vasconcelos, Wilson A. Silva, Luiz Lehmann Coutinho, Dominique García
Software Mentions: 1
Published: over 10 years ago