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8
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2
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777
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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
21 days ago by David Langenberger 11k
3
votes
2
replies
566
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
28 days ago by Johannes W. Dietrich • 0
12
votes
2
replies
443
views
News: 8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024) - already half booked
Workshop RNA-Seq DNA-Seq Illumina
16 days ago by David Langenberger 11k
0
votes
0
replies
204
views
News: Online course: Reproducibility in Bioinformatics
Singularity Version-Control Docker Containers
updated 28 days ago by 43k • written 28 days ago by ★ 2.5k
0
votes
0
replies
189
views
News: Online course: Meta-analysis in R
Meta-Analysis Statistics R
updated 8 days ago by 43k • written 8 days ago by ★ 2.5k
0
votes
0
replies
183
views
News: Online course: Meta-analysis in R
Meta-Analysis R
updated 14 days ago by 43k • written 15 days ago by ★ 2.5k
0
votes
0
replies
177
views
News: Online course: Network Analysis in R
NetworkAnalyis R
12 days ago by carlopecoraro2 ★ 2.5k
0
votes
0
replies
175
views
News: Course - Agent-Based Modelling Using NetLogo - University of Lodz, Poland
Netlogo Individual-Based-Models Agent-Based-Models
updated 8 days ago by 43k • written 8 days ago by ★ 2.5k
1
vote
0
replies
173
views
News: Landscape Genomics course in Switzerland
LFMM Landscape-Genomics Sambada R Local-Adaptation
updated 18 days ago by 43k • written 20 days ago by ★ 2.5k
0
votes
0
replies
173
views
News: Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
workshop RNA-seq nextflow DNA-seq
updated 10 days ago by 43k • written 10 days ago by 11k
0
votes
0
replies
167
views
News: Online course: Analysis of Prokaryotic Pangenomes (Last call)
Prokaryotic Bacterial-Genomics Pangenomics
updated 28 days ago by 43k • written 28 days ago by ★ 2.5k
0
votes
0
replies
145
views
News: Online course: Eukaryotic Metabarcoding
Metabarcoding Biodiversity R eDNA
25 days ago by carlopecoraro2 ★ 2.5k
0
votes
0
replies
143
views
News: Online course: Food Traceability Using Genomic Tools
Nanopore Genomic-Tools Illumina Food-Traceability
updated 22 days ago by 43k • written 23 days ago by ★ 2.5k
0
votes
0
replies
142
views
News: Deadline Approaching: PETs for Public Health Challenge
privacy public-health-challenge
updated 11 days ago by 43k • written 11 days ago by ▴ 380
0
votes
0
replies
130
views
News: upcoming online statistical courses
Statistics R Data-Analysis
updated 5 days ago by 43k • written 5 days ago by ★ 2.5k
1
vote
0
replies
128
views
News: Online Live Course: Introduction to Machine Learning in R
Rstats TScourses Rlang Rproject
updated 15 days ago by 43k • written 15 days ago by ▴ 70
2
votes
0
replies
123
views
News: Online Course Introduction to Network Analysis and Modelling
Python Network-Analysis
updated 15 days ago by 43k • written 15 days ago by ▴ 70
2
votes
0
replies
123
views
News: Online Course Generalised Additive Mixed Models (GAMM): modelling space-time correlation structures
GAMM Rlang Rstats Rproject
updated 15 days ago by 43k • written 15 days ago by ▴ 70
0
votes
0
replies
119
views
News: Online course: Multivariate Data Analysis with R and vegan
Multivariate-Statistics vegan R
updated 18 days ago by 43k • written 18 days ago by ★ 2.5k
2
votes
0
replies
116
views
News: Online course: Genome Annotation
Genome-Assembly RNA-seq Genome-Annotation
updated 16 days ago by 43k • written 16 days ago by ★ 2.5k
3
votes
0
replies
114
views
News: Interested in Spatial Omics?
Bioconductor Spatial-Omics Spatial-Transcriptomics
updated 3 days ago by 43k • written 3 days ago by ★ 2.5k
2
votes
0
replies
114
views
News: Course Functional Programming with R
Rstats TScourses Rproject KeepLearning Rlang
16 days ago by Transmitting Science communication ▴ 70
0
votes
0
replies
112
views
News: 8th Berlin Summer School in NGS Data Analysis - Apply Now
DNA-seq variant-calling RNA-seq illumina transcriptomics
updated 21 hours ago by 43k • written 2 days ago by 11k
0
votes
0
replies
109
views
News: hands-on introduction to generalized linear models (GLMs) using R
Generalized-Linear-Models GLM R
updated 1 day ago by 43k • written 2 days ago by ★ 2.5k
0
votes
0
replies
82
views
News: Online course: DNA methylation
Pacbio Nanopore DnaMethylation Evolution
4 days ago by carlopecoraro2 ★ 2.5k
3
votes
0
replies
76
views
News: Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy scRNA Machinelearning GenerativeAI
7 hours ago by Claire Watson ▴ 60
0
votes
0
replies
74
views
News: Master Meta-analysis with R (May 13-16) - Online!
Meta-Analysis Statistics R
updated 21 hours ago by 43k • written 1 day ago by ★ 2.5k
27 results • Page 1 of 1
Recent Votes
Comment: Convert SAM to BAM
Comment: Should I use unpaired reads from trimmomatic
Answer: Should I use unpaired reads from trimmomatic
A: Mean Variance Relationship single cell RNA-Seq Data
Answer: Blasting two protein sequences vs two nucleotide sequences
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
how to combine multiple RNAseq count files into a single dataframe in R and unix
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Recent Awards • All
Scholar to GenoMax 141k
Popular Question to rheab1230 ▴ 140
Popular Question to BioinfGuru ★ 1.7k
Scholar to bk11 ★ 2.4k
Popular Question to vinayjrao ▴ 250
Supporter to Jalil Sharif ▴ 80
Popular Question to sil_bioinfo ▴ 40
Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by BioinfGuru ★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon by i.sudbery 19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt by sapuizait ▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question by bk11 ★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon by GenoMax 141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File? by cmdcolin ★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon by Patadu94 • 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon by Patadu94 • 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq by pinheirofabiano ▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon by Patadu94 • 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
Answer: Create a new bed file with all pairwise combinations between two other bed files by Pierre Lindenbaum 161k
bedtools intersect \ -a <(sort -t $'\t' -k1,1 -k2,2n A.bed) \ -b <(awk '{X=250000;P=int($2);printf("%s\t%d\…
Comment: Create a new bed file with all pairwise combinations between two other bed files by J • 0
The command lines I wrote out for you are the ones I actually used. My original reference to bedtools intersect was because I assumed the b…
Comment: ScRNA data question by starswillfade ▴ 10
I just thought it was weird that considering each dot is a cell their expressions were all on a single line instead of being spread out lik…
Comment: ScRNA data question by starswillfade ▴ 10
![enter image description here][1] I am already using Seurat V5 I think. I am using SCTransform as it was recommended by the seurat page. I…
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