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143 results • Page 3 of 3
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Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
0
replies
684
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
0
votes
0
replies
235
views
Tutorial: How to Label the Y Axis with percentage sign and Order Bars in ggplot2 using a single cell dataset
seurat single-cell ggplot2
3 months ago by Ming Tommy Tang ★ 3.9k
2
votes
0
replies
566
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 7 months ago by 43k • written 7 months ago by 161k
0
votes
0
replies
670
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
10 months ago by Coremine Medical ▴ 20
1
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0
replies
177
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
10 days ago by Novogene ▴ 420
4
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0
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953
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
12 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
312
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
2
votes
0
replies
1.4k
views
Tutorial: Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq next-gen
updated 11 months ago by 43k • written 5.9 years ago by ▴ 340
0
votes
0
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2.9k
views
Tutorial: Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test R Autocorrelation Breusch-Godfrey
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
1
vote
0
replies
1.7k
views
Tutorial: Using Subversion to update /devel branch of Bioconductor package
bioconductor subversion
updated 11 months ago by 43k • written 6.7 years ago by ▴ 350
0
votes
0
replies
246
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
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0
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3.6k
views
Tutorial: SFA (Stochastic Frontier Analysis) STATA 14
R
updated 11 months ago by 43k • written 6.2 years ago by ▴ 10
1
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0
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342
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
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314
views
Tutorial: How to convert sra files to fastq files using parallelized fastq-dump
fastq sra
3 months ago by Ming Tommy Tang ★ 3.9k
7
votes
0
replies
595
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
8 months ago by barslmn ★ 2.1k
1
vote
0
replies
532
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
8 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
1.4k
views
Tutorial: Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by 43k • written 6.3 years ago by ▴ 90
0
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0
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3.1k
views
Tutorial: Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test R-Commander
updated 11 months ago by 43k • written 6.4 years ago by ▴ 10
1
vote
0
replies
516
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
6 months ago by Ming Tommy Tang ★ 3.9k
2
votes
0
replies
2.1k
views
Tutorial: How to display Agilent CGH array in IGV
IGV CGH
updated 11 months ago by 43k • written 6.4 years ago by ★ 2.4k
5
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0
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2.2k
views
Tutorial: Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm meme parallel
updated 11 months ago by 43k • written 6.6 years ago by 35k
6
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0
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535
views
Tutorial: 12 useful command line tools and tricks for genomics data science
unix
updated 12 weeks ago by 11k • written 12 weeks ago by ★ 3.9k
0
votes
0
replies
463
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
5 months ago by rohitsatyam102 ▴ 850
2
votes
0
replies
473
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
1
vote
0
replies
684
views
Tutorial: How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix scRNA-seq single-cell rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
0
votes
0
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217
views
Tutorial: Parsing HMMER output
HMMER
updated 5 weeks ago by 141k • written 5 weeks ago by ▴ 140
1
vote
0
replies
325
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
273
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
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0
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256
views
Tutorial: Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python RNA-seq batch-correction
updated 3 months ago by 43k • written 3 months ago by ▴ 120
2
votes
0
replies
208
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
8 weeks ago by Novogene ▴ 420
1
vote
0
replies
274
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
0
replies
634
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
4
votes
0
replies
775
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
10 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
651
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
10 months ago by sinha.shriprakash ▴ 20
2
votes
0
replies
709
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 10 months ago by 43k • written 10 months ago by ▴ 20
1
vote
0
replies
2.6k
views
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo R data-mining differential-gene-expression RNA-Seq
updated 10 months ago by 43k • written 16 months ago by ▴ 420
0
votes
0
replies
677
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
8 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
370
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 850
4
votes
0
replies
2.3k
views
Tutorial: Accurate prediction of active enhancers using PARE
ChIP-Seq histone-modification enhancer
updated 11 months ago by 43k • written 7.0 years ago by ▴ 100
0
votes
0
replies
665
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 10 months ago by 43k • written 10 months ago by ★ 3.9k
2
votes
0
replies
3.2k
views
Tutorial: How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix Seurat single-cell rstats
updated 9 months ago by 43k • written 9 months ago by ★ 3.9k
2
votes
0
replies
6.9k
views
Tutorial: How to - Install Python packages in a virtual environment (virtualenv)
ubuntu cutadapt virtualenv python windows
updated 11 months ago by 43k • written 6.4 years ago by ▴ 320
143 results • Page 3 of 3
Recent Votes
How to input margin to UpsetR figure
Comment: How to assign cell types after integration in scRNA
NGS forensics: how to know if data is fabricated
Answer: ChIP-seq datasets: input samples omitted?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
A: Deeptools plotHeatmap - Maintain Order of Input BED file
Comment: NGS forensics: how to know if data is fabricated
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Recent Replies
Comment: Downloading full alignments from Pfam by GenoMax 141k
Not as convenient but the entire set of full alignments can be downloaded here: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pf…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
> What does clipped Fastq mean? Probably means that NCBI has already scanned and trimmed adapter sequencers. > both forward and revers…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
You can use the default `adapters.fa` file included in the `resources` folder of [**BBMap suite**][1] (program to use is `bbduk.sh`) or a p…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
Only way to find out is to try. It may work but if it is not going to then you will find that out quick (process would likely crash because…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Also, there is no mention of adapter sequence so which adapter sequence should i use to remove it from some other reads?
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Also, Do you think i can reproduce at least most part of the data from the paper just on my laptop? It has 4 logical processors (Intel(R) C…
Comment: NGS forensics: how to know if data is fabricated by Philipp Bayer 8.3k
While I think this is an interesting case, I've before found cleaned 'raw' data on SRA. It happens: bioinformaticians receive the raw data,…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
1. What does clipped Fastq mean? both forward and reverse reads in the same file? 2. Why would you remove 2000bp contigs? I feel it will gi…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Well, I downloaded both the reads from-[LINK][1]. Thats all i did. Thats the only thing i need to do, right? I'l try spades. [1]: http…
Comment: How to assign cell types after integration in scRNA by Francesco ▴ 10
Thanks for the fast reply.. however i had only partially understood the answer. Is correct saying that low-representation integration and b…
Answer: Can I run cellassign on samples independently if there is batch effect present? by Francesco ▴ 10
Hi! Whenever you do make independent analysis or aggregate data and analyze them, most cell type assignment tools start from raw counts to …
Comment: gvcf joint calling by zihanss • 0
Thanks for your comment, I get it now.
Answer: ChIP-seq datasets: input samples omitted? by ATpoint 82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA by ATpoint 82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
Comment: Differential Expression using Isoseq-supplemented reference transcriptome by gaoanwei • 0
I found the question and ASK the GPT4 turbo
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