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76
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71
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19k
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19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 1 day ago by 141k • written 6.2 years ago by 87k
5
votes
13
replies
1.0k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 3 days ago by 81k • written 4 days ago by ★ 1.7k
7
votes
3
replies
2.8k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 4 days ago by 6.4k • written 15 months ago by ▴ 130
1
vote
0
replies
165
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
5 days ago by Novogene ▴ 420
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 5 days ago by • 0 • written 3.5 years ago by 3.2k
49
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 26 days ago by 100k • written 8.1 years ago by 43k
10
votes
6
replies
4.1k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 27 days ago by 43k • written 6.2 years ago by 87k
0
votes
0
replies
205
views
Tutorial: Parsing HMMER output
HMMER
updated 4 weeks ago by 141k • written 4 weeks ago by ▴ 140
34
votes
16
replies
20k
views
14 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 5 weeks ago by ▴ 30 • written 7.6 years ago by ▴ 310
70
votes
29
replies
15k
views
13 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 5 weeks ago by ★ 1.2k • written 5.1 years ago by 16k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 6 weeks ago by • 0 • written 3.6 years ago by 3.2k
2
votes
0
replies
196
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
8 weeks ago by Novogene ▴ 420
3
votes
0
replies
216
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
8 weeks ago by Novogene ▴ 420
6
votes
0
replies
522
views
Tutorial: 12 useful command line tools and tricks for genomics data science
unix
updated 11 weeks ago by 11k • written 11 weeks ago by ★ 3.9k
0
votes
0
replies
302
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
1
vote
5
replies
603
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
3
votes
2
replies
523
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by 81k • written 3 months ago by ▴ 120
2
votes
1
reply
390
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
1
reply
283
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
238
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
240
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
1
vote
0
replies
262
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
0
votes
0
replies
263
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
1
vote
0
replies
323
views
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
0
votes
0
replies
221
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
1
vote
0
replies
269
views
Tutorial: How to Use Biomart to Find Mouse Orthologs for Human Genes
ids gene bioconductor
3 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
298
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
0
votes
1
reply
527
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
2
votes
0
replies
392
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
0
replies
238
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
1
vote
1
reply
318
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 3 months ago by 43k • written 3 months ago by ▴ 120
2
votes
3
replies
550
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
6
votes
1
reply
426
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 3 months ago by ▴ 120
0
votes
0
replies
244
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
39
votes
16
replies
36k
views
16 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 3 months ago by 141k • written 3.7 years ago by ▴ 160
1
vote
0
replies
330
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
3
votes
3
replies
1.1k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 3 months ago by ▴ 40 • written 8 months ago by ★ 3.9k
16
votes
3
replies
4.3k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 3.1 years ago by • 0 • written 3.6 years ago by 3.2k
0
votes
0
replies
349
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 4 months ago by 43k • written 4 months ago by ★ 3.9k
1
vote
0
replies
316
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
362
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 840
0
votes
0
replies
454
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
5 months ago by rohitsatyam102 ▴ 840
0
votes
4
replies
722
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
5 months ago by Coremine Medical ▴ 20
90
votes
48
replies
33k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 5 months ago by 43k • written 10.5 years ago by ★ 7.8k
1
vote
0
replies
507
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
5 months ago by Ming Tommy Tang ★ 3.9k
10
votes
31
replies
11k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 6 months ago by • 0 • written 6.3 years ago by ▴ 320
2
votes
0
replies
560
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
1
reply
522
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 7 months ago by 81k • written 7 months ago by ▴ 30
4
votes
2
replies
2.8k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 7 months ago by 141k • written 4.0 years ago by 81k
0
votes
0
replies
666
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
410 results • Page 1 of 9
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Recent Replies
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
Ah I see that in now. I am not sure why MGI has split the whitelist into two sections. You may need to see if you can dig up some info abou…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
read 1 is 30bp... which I think you meant to type. If you scroll approximately halfway down the json file I linked to, it has the following…
Comment: TCGA2STAT Error: Firehose connection by Ram 43k
The package has been removed from CRAN and BioConductor. Should you even be using it?
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
The barcodes are in location 1-10 and you have the actual list there. I don't know for certain what is in position 11-20 (perhaps spacer, c…
Answer: Including plasmid in transcriptome assemblies by GenoMax 141k
> I want to use both STAR and BOWTIE2 for assembly Those programs are aligners not assemblers. But since you are working with bacteria yo…
Comment: How to slice a gvcf file with tabix? by Sd • 0
I already have gvcfs called by chromosome and there are 24 gvcfs per sample which I merged them into a single gvcf per sample. Now I want …
Comment: Find subcluster under a cluster, find differential genes in one cluster between by bk11 ★ 2.3k
First, could you please explain any reason for not using Seurat V5 approach for your data integration mentioned in [here][1]? > Now moving…
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by atowns21 • 0
So I'd take the json file located [here][1] and essentially create the whitelist to be all possible combinations of the position 1-10 barco…
Comment: TCGA2STAT Error: Firehose connection by Ngrin • 0
Hey Gnana, could you find a way to solve the issue? I have the same error
Comment: How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq librarie by GenoMax 141k
You simply need to make a list of barcodes one on each line: https://kb.10xgenomics.com/hc/en-us/articles/115004506263-What-is-a-barcode-wh…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by GenoMax 141k
> What specifications and operating system would be ideal for my case? For choice of OS: Linux to access the large pool of open source sof…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
Ok. First update your phenotypes because in the 6th column all the values are -9 meaning missing, and then run `--assoc`. You can do the fo…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by i.sudbery 19k
You'll probably get away with using one of the other analysis pipelines, like Alevin-fry with much less than 128GB of RAM. Workstations can…
Comment: Difference between samtools "-f 9" and "-f 11" by Dylan • 0
> (which is weird, if it's in proper pair, read and its mate should be both mapped) So that was my thought as well, I think the code you l…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by Ram 43k
> several single cell samples At the same time? You need a server, not a PC. Google around (and search the site as well with keyword "conf…
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