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Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 11 months ago by 44k • written 17 months ago by ▴ 420
1
vote
0
replies
322
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq SCSA
updated 4 months ago by 44k • written 4 months ago by ▴ 120
2
votes
0
replies
493
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 10 months ago by 44k • written 10 months ago by ★ 3.9k
1
vote
0
replies
389
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
2
votes
0
replies
1.2k
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 6 months ago by • 0 • written 16 months ago by ★ 1.6k
1
vote
0
replies
708
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 10 months ago by 44k • written 10 months ago by ★ 3.9k
1
vote
0
replies
384
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
5 months ago by Ming Tommy Tang ★ 3.9k
7
votes
0
replies
619
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
9 months ago by barslmn ★ 2.2k
2
votes
0
replies
740
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 11 months ago by 44k • written 11 months ago by ▴ 20
1
vote
0
replies
233
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
5 weeks ago by Novogene ▴ 420
0
votes
0
replies
709
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 11 months ago by 44k • written 11 months ago by ★ 3.9k
0
votes
0
replies
366
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
1
vote
0
replies
705
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 11 months ago by 44k • written 11 months ago by ★ 3.9k
1
vote
0
replies
627
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
11 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
424
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 5 months ago by 44k • written 5 months ago by ★ 3.9k
0
votes
0
replies
272
views
Tutorial: Parsing HMMER output
HMMER
updated 9 weeks ago by 142k • written 9 weeks ago by ▴ 140
0
votes
0
replies
283
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
4 months ago by Ming Tommy Tang ★ 3.9k
6
votes
0
replies
595
views
Tutorial: 12 useful command line tools and tricks for genomics data science
unix
updated 3 months ago by 11k • written 3 months ago by ★ 3.9k
4
votes
0
replies
797
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
11 months ago by Ming Tommy Tang ★ 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 10 months ago by 44k • written 10 months ago by ★ 3.9k
3
votes
0
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257
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
12 weeks ago by Novogene ▴ 420
0
votes
0
replies
320
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
2
votes
0
replies
603
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 8 months ago by 44k • written 8 months ago by 162k
0
votes
0
replies
503
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
6 months ago by rohitsatyam102 ▴ 870
0
votes
0
replies
304
views
Tutorial: Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python RNA-seq batch-correction
updated 4 months ago by 44k • written 4 months ago by ▴ 120
2
votes
0
replies
240
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
12 weeks ago by Novogene ▴ 420
1
vote
0
replies
368
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
670
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
11 months ago by sinha.shriprakash ▴ 20
1
vote
0
replies
2.7k
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 11 months ago by 44k • written 17 months ago by ▴ 420
0
votes
0
replies
703
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
9 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
400
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
6 months ago by rohitsatyam102 ▴ 870
0
votes
0
replies
297
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq SCSA
updated 4 months ago by 44k • written 4 months ago by ▴ 120
1
vote
0
replies
566
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
9 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
315
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
1
vote
0
replies
655
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 9 months ago by 44k • written 9 months ago by ★ 3.9k
0
votes
0
replies
353
views
Tutorial: How to convert sra files to fastq files using parallelized fastq-dump
fastq sra
4 months ago by Ming Tommy Tang ★ 3.9k
1
vote
0
replies
846
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 6 months ago by 44k • written 14 months ago by ▴ 10
3
votes
0
replies
769
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
11 months ago by Ming Tommy Tang ★ 3.9k
5
votes
0
replies
1.7k
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 11 months ago by 44k • written 17 months ago by ▴ 420
1
vote
0
replies
320
views
Tutorial: How to Use Biomart to Find Mouse Orthologs for Human Genes
ids gene bioconductor
4 months ago by Ming Tommy Tang ★ 3.9k
2
votes
0
replies
3.3k
views
Tutorial: use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene slicer fastq splitter
updated 11 months ago by 44k • written 6.6 years ago by ★ 2.5k
91 results • Page 2 of 2
Recent Votes
Answer: ComplexHeatmap - How to change fontsize of rowAnnotation
Comment: Harmony integration group.by.var parameter
Answer: Harmony integration group.by.var parameter
A: Blast - Formatting Output
Answer: Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
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Recent Replies
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
This works. Thank you so so much!
Comment: Harmony integration group.by.var parameter by jared.andrews07 ★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter by Picasa ▴ 640
Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea by sc_analysis • 0
I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data by Sara ▴ 30
Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files by Deepthi • 0
I unzipped the fastq files to check whether reads are trimmed adapter or not. I have checked the quality control using fastqc they are go…
Comment: Mutation counts corrected by number of samples by Ram 44k
> I want to compare the number of mutations This comparison will give you literally no useful information.
Answer: How to scrape BioMart data from https://sorfs.ugent.be/ website by Pierre Lindenbaum 162k
something like: seq 1 100 4377380 | while read F ; do wget --no-check-certificate -O - "https://sorfs.ugent.be/database/micrope…
Answer: Harmony integration group.by.var parameter by jared.andrews07 ★ 17k
The variability explained by the variables provided to `group.by.vars` is what Harmony will try to remove. Assuming you want to remove the …
Answer: Why some SNP's allele frequencies in gnomAD are so different between v2 and v4? by Jeremy Leipzig 22k
That SNP is in an HLA gene which has had a lot of attention and improvement over the years, ranging from kits to software to the reference …
Comment: Overlapping clusters for different biological conditions: Seurat, UMAP by Bastien Hervé 5.3k
What is the need of PBMC in your analysis ? If none, removing them from the beginning will allow your clusters to be more specific to your …
Answer: How to calculate cell type frequency between two groups in single cell data by Bastien Hervé 5.3k
I believe `sample_id` are your replicates in either `patient` or `control`. You can do it manually by normalizing the number of cells yo…
Answer: bfctools merge [E::hts_open_format] Failed to open file by j.f.akers • 0
I think the program is trying to open a .vcf.gz.csi file rather than the actual data which is the .vcf.gz file, the csi file is not data, j…
Comment: LDhat lookup table by NÚRIA • 0
Hi! Did you manage to fix this? I run convert successfully on 60 unphased diploid samples (1500bp), hence I used lktable available in LDh…
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI by F110152169 • 0
It's Parkinson's disease. How do I get the right order?
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