Aedin Culhane

@AedinCulhane

Prof

@MedicineAtUL

, Computational immune oncology #bioinformatics, #biostatistics, #rstats, R,

@bioconductor

, women in STEM, parents in STEM, Tweets are my own

Medical & HealthHorse and Groomlinkedin.com/in/aedinculhaneJoined September 2012

2,551 Following

3,402 Followers

Aedin Culhane’s Tweets

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Aedin Culhane

@AedinCulhane

Dec 1, 2021

Delighted to introduce correspondence analysis of scRNAseq. We show CA of Freeman-Tukey residuals outperforms CA of the Pearson Residuals corral: Single-cell RNA-seq dimension reduction, batch integration, and visualization with correspondence analysis

biorxiv.org

corral: Single-cell RNA-seq dimension reduction, batch integration, and visualization with corres...

Effective dimension reduction is an essential step in analysis of single cell RNA-seq (scRNAseq) count data, which are high-dimensional, sparse, and noisy. Principal component analysis (PCA) is...

163

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Aedin Culhane Retweeted

Zuguang Gu

@jokergoo_gu

Jul 28

This is the link of my cola package demo presentation on #bioc2022: docs.google.com/presentation/d Two repos related to the presentation: github.com/jokergoo/cola_

github.com

GitHub - jokergoo/cola: A General Framework for Consensus Partitioning

A General Framework for Consensus Partitioning. Contribute to jokergoo/cola development by creating an account on GitHub.

Aedin Culhane Retweeted

Sean Davis

@seandavis12

Jul 30

The #bioc2022 conference by the numbers. Thanks to dozens of folks who put the conference together. Materials and videos will be linked at: bioc2022.bioconductor.org

Aedin Culhane Retweeted

Leonardo Collado-Torres

@lcolladotor

Jul 29

Next up Ava Jensen on #NMF (non-negative matrix factorization) with #RcppML: over 10 times faster ‼️ #bioc2022

⁦

⁩ project leader Vince Carey thanks sponsors especially platinum sponsors ⁦

@moderna_tx

⁩ and ⁦

@nanostringtech

⁩ at #bioc2022 closing session. Amazing how many dedicated people are here at past 5:30pm on a sunny Friday. What a great community

Aedin Culhane

@AedinCulhane

Jul 30

Awesome Erica takes the stage for closing remarks at #bioc2022. ⁦

@Bioconductor

⁩

Topics to follow

Carousel

Vince Carey and

presenting on GPU in

and how to easily do this via AnVil and

@TerraBioApp

#bioc2022

Aedin Culhane

@AedinCulhane

Jul 29

Hervé Pagès package SparseArray is way efficient, faster than dgCMatrix sparse matrix objects, and can accommodate 2D, 3D or arrays, integers, double, string or logicals #RStats

@Bioconductor

github.com/Bioconductor/S

Aedin Culhane

@AedinCulhane

Jul 29

Hervé Pagès describe the fast #rstats package in

@bioconductor

that can compute matrix summarisation operations (rowSums, colSums, rowMeans etc) for sparse matrices in R (dgCMatrix objects) but described limitations and improvements in S4Arrays::SparseArray #bioc2022

Aedin Culhane

@AedinCulhane

Jul 29

Alexandru Mahmoud is presenting helm and

@kubernetesio

for

@Bioconductor

github.com/Bioconductor/b. #bioc2022

Great point. The

community is diverse and multi-talented. You don't have to write a package to be a valuable contributor. Erica is a Program Manager and Event Coordinator at

@dfcidatascience

and her contribution to organisation of Bioconductor meetings is essential

Quote Tweet

Kyle Cuilla

@kc_analytics

· Jul 28

Reminder: you don’t have to write a package to be a valuable contributor to the #rstats community

Aedin Culhane Retweeted

Kyle Cuilla

@kc_analytics

Jul 28

Reminder: you don’t have to write a package to be a valuable contributor to the #rstats community

110

Apply to be a

Certified

instructor. We are now accepting applications to attend a training course

bioconductor.github.io

Bioconductor community blog: Bioconductor becomes a Carpentries member organization

Starting from August 1, 2022, Bioconductor will be a member of The Carpentries. Among other things, the membership enables us to allow 15 individuals to follow the Carpentries' Instructor Training...

Aedin Culhane

@AedinCulhane

Jul 28

Excited. From Aug 1st

@Bioconductor

will be a member of

@thecarpentries

a global community who develop and teach interactive, hands-on workshops on computing and data skills. We'll train 15 instructors per year with funding from

@cziscience

Info: bioconductor.github.io/biocblog/posts #bioc2022

bioconductor.github.io

Bioconductor community blog: Bioconductor becomes a Carpentries member organization

Starting from August 1, 2022, Bioconductor will be a member of The Carpentries. Among other things, the membership enables us to allow 15 individuals to follow the Carpentries' Instructor Training...

Aedin Culhane

@AedinCulhane

Jul 28

Erdal Cosgun explains how to use

@MSFTGenomics

custom VM to make cloud-based #bioinformatics

@Bioconductor

simpler #bioc2022 github.com/microsoft/geno

Aedin Culhane

@AedinCulhane

Jul 28

Massive congratulations to the four recipients of a ⁦⁦

@bioconductor

Award in 2022. These prestigious awards are nominated by the community for their contribution to

@Bioconductor

. Congrats ⁦

@seandavis12

, Nicole Kramer, Erica Feick, Hervé Pagès. #bioc2022

Aedin Culhane

@AedinCulhane

Jul 28

Massive congratulations to the four recipients of a ⁦⁦Bioc⁩ Award in 2022. These prestigious awards are nominated by the community for their contribution to ⁦

@Bioconductor

⁩. Congrats ⁦

@seandavis12

⁩, Nicole Kramer, Erica Feick, and Hervé Pagès. #bioc2022

Aedin Culhane

@AedinCulhane

Jul 28

Incredibly well deserved

Massive congratulations Hervé Pagès #bioc2022 bioc awardee, as member of the core team he has made a massive contribution to the project.

Aedin Culhane

@AedinCulhane

Jul 28

Congratulations Nicole Kramer a #bioc2022 bioc awardee for her excellent

@Bioconductor

new package plotgardener which has great documentation bioconductor.org/packages/3.15/

Aedin Culhane

@AedinCulhane

Jul 28

Congratulations Erica Feick #bioc2022 bioc awardee.

⁦

⁩ mentioned they have positions at all levels in their department #bioc2022

Aedin Culhane Retweeted

Tim Triche, Jr.

@timtriche

Jul 28

Also: a key feature of the

@bioconductor

community is genuine peer review.

@SherlockpHolmes

reminding us that a random package on GitHub (even a Bioconductor GitHub package) isn’t a BioC package.

@nanostringtech

chiming in to note that this isn’t just a DOI; it’s security & build

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Aedin Culhane Retweeted

Tim Triche, Jr.

@timtriche

Jul 28

New this year, a BioC CAB working group for moving to the Dark Side! Led by Nicole Ortogero

@nanostringtech

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Aedin Culhane Retweeted

Tim Triche, Jr.

@timtriche

Jul 28

Full Bioconductor CAB: bioconductor.org/about/communit

WebEx outage impacting #bioc2022. Keynote of ⁦

@jalees_rehman

⁩ delayed a few minutes

Aedin Culhane Retweeted

Ibrahim I. Taskiran

@ibrahimihsan

Jul 27

We then exploited this concept further by creating “dual-code” enhancers that target two cell types. Starting from a genomic enhancer, we added a second code into the same sequence and expanded its spatial activity to another cell-type. (4/n)

Interesting study on enhancers

Quote Tweet

Ibrahim I. Taskiran

@ibrahimihsan

· Jul 27

Thrilled to share my ultimate PhD project at @steinaerts' lab on designing cell-type specific synthetic enhancers! We implemented three different design strategies guided by our previously trained deep learning models on fly brain enhancers. Link: bit.ly/3oAILXS (1/n)

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Aedin Culhane Retweeted

is giving an amazing talk on

@Bioconductor

Docker images for multi-node parallel computing on the cloud at #Bioc2022. Don't miss it!

Aedin Culhane Retweeted

Jared Andrews

@JMA_Data

Jul 27

Very good demo for multiplexed spatial analysis by

@NilsEling

at #BioC2022: bodenmillergroup.github.io/demos/ Straightforward image segmentation, ingest into R, analysis, and viz.

Aedin Culhane Retweeted

Javier Santoyo

@jsantoyo

Jul 28

Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures. #LongRead #RNA #Sequencing #BioinformaticsAnalysis #ToolsBenchmarking #DataSets #Bioinformatics biorxiv.org/content/10.110

@biorxivpreprint

biorxiv.org

Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures

The current lack of benchmark datasets with inbuilt ground-truth makes it challenging to compare the performance of existing long-read isoform detection and differential expression analysis workflo...

Aedin Culhane Retweeted

RStudio

@rstudio

Jul 28

We're excited to announce Quarto, a new open-source scientific and technical publishing system. Quarto is the next generation of R Markdown and takes what we've learned from the last 10 years and weave it into a more complete, cohesive whole. Read more: