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News: FINAL CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell sequencing
19 days ago by David Langenberger 11k
3
votes
2
replies
553
views
News: Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Vol…
mathematical-modelling endocrinology ML systems-biology machine-learning
26 days ago by Johannes W. Dietrich • 0
12
votes
2
replies
439
views
News: 8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024) - already half booked
Workshop RNA-Seq DNA-Seq Illumina
14 days ago by David Langenberger 11k
0
votes
0
replies
198
views
News: Online course: Reproducibility in Bioinformatics
Singularity Version-Control Docker Containers
updated 27 days ago by 43k • written 27 days ago by ★ 2.5k
0
votes
0
replies
184
views
News: Online course: Meta-analysis in R
Meta-Analysis Statistics R
updated 6 days ago by 43k • written 6 days ago by ★ 2.5k
0
votes
0
replies
181
views
News: Online course: Meta-analysis in R
Meta-Analysis R
updated 12 days ago by 43k • written 13 days ago by ★ 2.5k
0
votes
0
replies
174
views
News: Online course: Network Analysis in R
NetworkAnalyis R
10 days ago by carlopecoraro2 ★ 2.5k
1
vote
0
replies
170
views
News: Landscape Genomics course in Switzerland
LFMM Landscape-Genomics Sambada R Local-Adaptation
updated 16 days ago by 43k • written 18 days ago by ★ 2.5k
0
votes
0
replies
170
views
News: Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo Individual-Based-Models Agent-Based-Models
updated 6 days ago by 43k • written 6 days ago by ★ 2.5k
0
votes
0
replies
170
views
News: Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
workshop RNA-seq nextflow DNA-seq
updated 8 days ago by 43k • written 8 days ago by 11k
0
votes
0
replies
161
views
News: Online course: Analysis of Prokaryotic Pangenomes (Last call)
Prokaryotic Bacterial-Genomics Pangenomics
updated 27 days ago by 43k • written 27 days ago by ★ 2.5k
0
votes
0
replies
143
views
News: Online course: Eukaryotic Metabarcoding
Metabarcoding Biodiversity R eDNA
23 days ago by carlopecoraro2 ★ 2.5k
0
votes
0
replies
140
views
News: Deadline Approaching: PETs for Public Health Challenge
privacy public-health-challenge
updated 9 days ago by 43k • written 9 days ago by ▴ 380
0
votes
0
replies
139
views
News: Online course: Food Traceability Using Genomic Tools
Nanopore Genomic-Tools Illumina Food-Traceability
updated 21 days ago by 43k • written 21 days ago by ★ 2.5k
1
vote
0
replies
126
views
News: Online Live Course: Introduction to Machine Learning in R
Rstats TScourses Rlang Rproject
updated 13 days ago by 43k • written 13 days ago by ▴ 70
0
votes
0
replies
126
views
News: upcoming online statistical courses
Statistics R Data-Analysis
updated 3 days ago by 43k • written 3 days ago by ★ 2.5k
2
votes
0
replies
121
views
News: Online Course Generalised Additive Mixed Models (GAMM): modelling space-time correlation structures
GAMM Rlang Rstats Rproject
updated 13 days ago by 43k • written 13 days ago by ▴ 70
2
votes
0
replies
118
views
News: Online Course Introduction to Network Analysis and Modelling
Python Network-Analysis
updated 13 days ago by 43k • written 13 days ago by ▴ 70
0
votes
0
replies
117
views
News: Online course: Multivariate Data Analysis with R and vegan
Multivariate-Statistics vegan R
updated 16 days ago by 43k • written 16 days ago by ★ 2.5k
2
votes
0
replies
113
views
News: Online course: Genome Annotation
Genome-Assembly RNA-seq Genome-Annotation
updated 15 days ago by 43k • written 15 days ago by ★ 2.5k
2
votes
0
replies
112
views
News: Course Functional Programming with R
Rstats TScourses Rproject KeepLearning Rlang
14 days ago by Transmitting Science communication ▴ 70
3
votes
0
replies
95
views
News: Interested in Spatial Omics?
Bioconductor Spatial-Omics Spatial-Transcriptomics
updated 1 day ago by 43k • written 1 day ago by ★ 2.5k
0
votes
0
replies
76
views
News: Online course: DNA methylation
Pacbio Nanopore DnaMethylation Evolution
2 days ago by carlopecoraro2 ★ 2.5k
0
votes
0
replies
54
views
News: hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models GLM R
updated 1 hour ago by 43k • written 13 hours ago by ★ 2.5k
0
votes
0
replies
40
views
News: 8th Berlin Summer School in NGS Data Analysis - Apply Now
variantcalling DNAseq illumina RNAseq transcriptomics
6 hours ago by David Langenberger 11k
25 results • Page 1 of 1
Recent Votes
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
A: Where To Download Pam50 Gene Set?
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Popular Question to daffodil ▴ 10
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Recent Replies
Comment: Creating Synthetic Sequences for a ML Model by biochugs • 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed) by Jeremy ▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination by DKA ▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed) by Mensur Dlakic ★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model by Mensur Dlakic ★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least additional problem on top of da…
Answer: PCA plot (Suggestions Needed) by Jeremy ▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file by GenoMax 141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination by GenoMax 141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file by Maria • 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination by haibol2017 ▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
Comment: How to trim transcripts using information from NCBI contamination screen report by GenoMax 141k
`bbduk.sh` can use the transcripts as input. There is a `adapters.fa` included in the `resources` directory of the distribution. You can do…
Comment: PCA plot (Suggestions Needed) by swbarnes2 14k
Cross posted here (including the code used to make up the counts): https://support.bioconductor.org/p/9157911/#9157959
Comment: To get p-values for the TPM by swbarnes2 14k
RSEM returns a kind of p-value if you run it with the "prior-enhanced" option. Did you do that? Are you completely sure that's the value y…
Comment: How to trim transcripts using information from NCBI contamination screen report by Lada ▴ 30
i checked both of these programs (`bbduk` and `fastp`) and it seems they use reads as inputs (fastq formats)... how can I trim my transcrip…
Comment: AGeNT LocatIt by barslmn ★ 2.1k
He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
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