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Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
11 hours ago by Novogene ▴ 410
85
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 20 hours 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 21 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 22 days ago by 43k • written 6.2 years ago by 87k
0
votes
0
replies
196
views
Tutorial: Parsing HMMER output
HMMER
updated 27 days ago by 141k • written 27 days 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 4 weeks ago by ▴ 30 • written 7.5 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 5 weeks ago by • 0 • written 3.5 years ago by 3.2k
2
votes
0
replies
193
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
7 weeks ago by Novogene ▴ 410
3
votes
0
replies
210
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
7 weeks ago by Novogene ▴ 410
6
votes
0
replies
501
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
295
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
593
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
512
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
383
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
277
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
234
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
233
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
256
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
257
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
316
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
215
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
264
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
288
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
521
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
380
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
230
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
310
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
534
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
419
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
234
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
328
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
3 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 7 months ago by ★ 3.9k
0
votes
0
replies
341
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
310
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
4 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
360
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
4 months ago by rohitsatyam102 ▴ 840
0
votes
0
replies
451
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
713
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
500
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 5 months ago by • 0 • written 6.3 years ago by ▴ 320
2
votes
0
replies
559
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
520
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 3.9 years ago by 81k
0
votes
0
replies
662
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
14
votes
3
replies
20k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 8 months ago by ▴ 30 • written 7.0 years ago by ★ 1.6k
8
votes
2
replies
1.1k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 8 months ago by 43k • written 8 months ago by ★ 2.5k
0
votes
0
replies
511
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
9
votes
4
replies
5.4k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
8 months ago by Hamid Ghaedi 3.2k
140 results • Page 1 of 3
Recent Votes
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
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Recent Replies
Comment: Downloaded pdb's on rcsb.org by Ram 43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
thank you so much
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org by Ram 43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need m…
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
thank you very much
Answer: Downloaded pdb's on rcsb.org by Ram 43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool by GenoMax 141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org by Ram 43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org by Ram 43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
Comment: DEG analysis of RNA-seq data across multiple tissues and two conditions by BioinfGuru ★ 1.7k
great guidance ... thank you
Comment: error in CPC2 by Ram 43k
Ashok, what is CPC2? Please edit your post and add as much context as you can.
Comment: python file for cpc2 by Ram 43k
Ashok - someone else had to (guess and) add context to your post. Please give us as much information as you can in the first place - we can…
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