Limit : this year
all time today this week this month this year
98 results • Page 1 of 2
Sort: Rank
Rank Views Votes Replies
7
votes
1
reply
216
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 14 days ago by 14k • written 14 days ago by ▴ 360
5
votes
5
replies
682
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 17 days ago by • 0 • written 26 days ago by ★ 3.9k
76
votes
72
replies
20k
views
19 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
26 days ago by Kevin Blighe 88k
5
votes
13
replies
2.1k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 4 weeks ago by 82k • written 4 weeks ago by ★ 1.7k
7
votes
3
replies
3.0k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 4 weeks ago by 6.4k • written 16 months ago by ▴ 130
1
vote
0
replies
227
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
4 weeks ago by Novogene ▴ 420
87
votes
24
replies
24k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 4 weeks ago by • 0 • written 3.6 years ago by 3.2k
50
votes
30
replies
12k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 7 weeks ago by 100k • written 8.2 years ago by 44k
10
votes
6
replies
4.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 7 weeks ago by 44k • written 6.3 years ago by 88k
0
votes
0
replies
265
views
Tutorial: Parsing HMMER output
HMMER
updated 8 weeks ago by 142k • written 8 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 9 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 9 weeks ago by ★ 1.2k • written 5.2 years ago by 16k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 10 weeks ago by • 0 • written 3.6 years ago by 3.2k
2
votes
0
replies
237
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
12 weeks ago by Novogene ▴ 420
3
votes
0
replies
257
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
12 weeks ago by Novogene ▴ 420
6
votes
0
replies
589
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
0
votes
0
replies
349
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
5
replies
684
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 4 months ago by 44k • written 4 months ago by ▴ 120
3
votes
2
replies
587
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 4 months ago by 82k • written 4 months ago by ▴ 120
2
votes
1
reply
486
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
1
reply
318
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
0
replies
271
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq SCSA
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
0
replies
294
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
317
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
0
votes
0
replies
311
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
1
vote
0
replies
381
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
0
votes
0
replies
278
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
1
vote
0
replies
315
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
0
votes
0
replies
358
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
0
votes
1
reply
589
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
2
votes
0
replies
448
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
1
vote
0
replies
310
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
1
vote
1
reply
386
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 4 months ago by 44k • written 4 months ago by ▴ 120
2
votes
3
replies
657
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
6
votes
1
reply
492
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 4 months ago by 44k • written 4 months ago by ▴ 120
0
votes
0
replies
299
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
39
votes
16
replies
37k
views
16 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 4 months ago by 142k • written 3.8 years ago by ▴ 160
1
vote
0
replies
380
views
Tutorial: 4 CITE-seq tutorials
CTIE-seq
4 months ago by Ming Tommy Tang ★ 3.9k
3
votes
3
replies
1.2k
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
updated 4 months ago by ▴ 40 • written 9 months ago by ★ 3.9k
0
votes
0
replies
421
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 5 months ago by 44k • written 5 months ago by ★ 3.9k
1
vote
0
replies
365
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
397
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 870
0
votes
0
replies
499
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
6 months ago by rohitsatyam102 ▴ 870
0
votes
4
replies
782
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
6 months ago by Coremine Medical ▴ 20
90
votes
48
replies
34k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 6 months ago by 44k • written 10.6 years ago by ★ 7.8k
1
vote
0
replies
560
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
10
votes
31
replies
11k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 7 months ago by • 0 • written 6.4 years ago by ▴ 320
2
votes
0
replies
601
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 161k
0
votes
1
reply
568
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 8 months ago by 82k • written 8 months ago by ▴ 30
4
votes
2
replies
3.0k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 8 months ago by 142k • written 4.0 years ago by 82k
98 results • Page 1 of 2
Recent Votes
Answer: tensorQTL interaction issue
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Answer: converting transcript IDs (Ensembl) to gene symbols in R
Comment: Trimming tool
Answer: Trimming tool
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
Recent Locations • All
Stony Brook University, NY, 1 minute ago
outer space, 2 minutes ago
United States, 3 minutes ago
United States, 3 minutes ago
Cambridge, MA, 8 minutes ago
Brazil, 9 minutes ago
Machhagan, 10 minutes ago
Recent Awards • All
Popular Question to Picasa ▴ 640
Supporter to Mol • 0
Popular Question to Rafael Soler ★ 1.2k
Teacher to shelkmike ★ 1.2k
Popular Question to applepie • 0
Popular Question to Peter Chung ▴ 200
Popular Question to ev97 ▴ 20
Recent Replies
Answer: Is it possible to run CibersortX with a very small number of samples? by finch • 0
Hi! I had a very similar issue and it's likely not at all related to your number of samples but to the format of your mixture file! Ciberso…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w by Ram 44k
You cannot *convert* a VCF to a FASTA as they have vastly different information content. Please explain your process - what exactly do you …
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o by Shukai • 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice by Zhenyu Zhang ★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice by Zhenyu Zhang ★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o by Ram 44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs by geneontologyhelp ▴ 400
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads) by Pierre Lindenbaum 161k
paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set by Matthias Zepper 4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R by bk11 ★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w by Pierre Lindenbaum 161k
well you try to use FastaAlternateReferenceMaker https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMak…
Comment: z-score of gene set by bk11 ★ 2.5k
Can you please tell us what will be your propose of z-score calculation?
Comment: DRAGEN gVCF files and joint calling GATK-GenomicsDB by DBScan ▴ 300
I think I did it once, but why would you use GATK with DRAGEN gVCF files? If you have a DRAGEN, the iterative gVCF Genotyper does a much fa…
Answer: Practical Haplotype Graph v2 not finding correct paths by beantkapoor16 ▴ 10
So, I just tested it and it's performing much better now. Most of the haplotype paths are coming from the expected haplotypes (australasica…
Comment: Kraken2 Custom Database non-deterministic results by Bjorn • 0
Thank you!
Traffic: 2877 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6