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141 results • Page 1 of 3
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7
votes
1
reply
154
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Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 3 days ago by 14k • written 3 days ago by ▴ 360
5
votes
5
replies
625
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 6 days ago by • 0 • written 15 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
15 days ago by Kevin Blighe 87k
5
votes
13
replies
1.7k
views
Tutorial: Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R Ubuntu Linux Bioconductor Rstudio
updated 20 days ago by 82k • written 21 days ago by ★ 1.7k
7
votes
3
replies
2.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 21 days ago by 6.4k • written 16 months ago by ▴ 130
1
vote
0
replies
207
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
22 days ago by Novogene ▴ 420
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 22 days ago by • 0 • written 3.6 years ago by 3.2k
50
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 6 weeks ago by 100k • written 8.2 years ago by 43k
10
votes
6
replies
4.2k
views
Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 6 weeks ago by 43k • written 6.2 years ago by 87k
0
votes
0
replies
243
views
Tutorial: Parsing HMMER output
HMMER
updated 7 weeks ago by 142k • written 7 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 7 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 8 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 8 weeks ago by • 0 • written 3.6 years ago by 3.2k
2
votes
0
replies
225
views
Tutorial: Premade library preparation – considerations, tips and tricks (II)
Illumina. Premade-library. NovaSeqX.
10 weeks ago by Novogene ▴ 420
3
votes
0
replies
244
views
Tutorial: Premade library preparation – considerations, tips and tricks (IA)
Premade-library Illumina NovaSeqX
10 weeks ago by Novogene ▴ 420
6
votes
0
replies
561
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
336
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
644
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
561
views
Tutorial: Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by 82k • written 3 months ago by ▴ 120
2
votes
1
reply
449
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
308
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
260
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
274
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
298
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
295
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
361
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
259
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
300
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
340
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
563
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 4 months ago by ▴ 120
2
votes
0
replies
430
views
Tutorial: Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
0
replies
269
views
Tutorial: Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
1
vote
1
reply
359
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 3 months ago by 43k • written 4 months ago by ▴ 120
2
votes
3
replies
623
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
6
votes
1
reply
471
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 3 months ago by 43k • written 4 months ago by ▴ 120
0
votes
0
replies
277
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 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 3.7 years ago by ▴ 160
1
vote
0
replies
360
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 8 months ago by ★ 3.9k
0
votes
0
replies
389
views
Tutorial: download metadata using GEOquery
computational-biology GEO metadata
updated 4 months ago by 43k • written 5 months ago by ★ 3.9k
1
vote
0
replies
345
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
5 months ago by Ming Tommy Tang ★ 3.9k
0
votes
0
replies
385
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 months ago by rohitsatyam102 ▴ 850
0
votes
0
replies
483
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
6 months ago by rohitsatyam102 ▴ 850
0
votes
4
replies
756
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 43k • written 10.6 years ago by ★ 7.8k
1
vote
0
replies
537
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 6 months ago by • 0 • written 6.3 years ago by ▴ 320
2
votes
0
replies
582
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
549
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
2.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 8 months ago by 142k • written 4.0 years ago by 82k
141 results • Page 1 of 3
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Comment: Can I readmap short reads to rDNA references?
Answer: EdgeR - relationship between logFC and coefficients
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Answer: Server or aws cloud- which one is better for gatk pipeline
Comment: Question about methylation location
Comment: Question about methylation location
Comment: Question about methylation location
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Recent Replies
Comment: Can I readmap short reads to rDNA references? by aniigodwinn • 0
Still on this, the reads are from org a, org b, and environmental contaminants. I have a fairly good idea what org b might be but i need to…
Comment: fastq screen aligner no specified. by Ximena • 0
Thank u so much, my OS is linux. I will try your advice.
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
No worries, I can completely appreciate that. I am having investigations similar to a condition causes by the RYR2 gene and was wondering i…
Comment: In IGV is this a heterogeneous mutation or false call? by Pierre Lindenbaum 161k
> RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sound stupid but does this make sense to what I've previousl…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
When click the blat it brings me to chr19 and mentions the RYR1 underneath although I was originally looking at the RYR2 gene. Sorry to sou…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Thanks for that! I'll try and have a look and see what is amiss if I can... In your opinion what do you feel is wrong in my alignment from…
Comment: In IGV is this a heterogeneous mutation or false call? by Pierre Lindenbaum 161k
yeah.. look at that, there is something wrong in your alignment, many reads were mapped in a location but they are all clipped, so somethin…
Comment: Custom Reference panel creation for data imputation from .vcf files by analyst ▴ 50
Hi [Kevin][1]! I have 80 samples of GBS data. I have called variants through GATK pipeline. Now I have to perform imputation. Do I need …
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Ah I've just found 'show soft clipped bases' and this is what comes up... how come it is all greyed out? ![enter image description here][…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
I've just displayed clipped bases and this is what it shows. Does this look right? ![enter image description here][1] ![enter imag…
Comment: In IGV is this a heterogeneous mutation or false call? by Tuck898 • 0
Hi, I really appreciate you taking the time to reply. I'm still learning with IGV and sorry to sound very inexperienced but how would I che…
Answer: In IGV is this a heterogeneous mutation or false call? by Pierre Lindenbaum 161k
there is a clear shift in the depth just close to this mutation, you should set IGV to display the clipped bases + check if there is a DUP …
Comment: Too many unpaired forward reads found by Trimmomatic by SilhouetteQ • 0
Using fastp, I found that the adapter sequence for the forward read is corresponding to Trans2_rc in the NexteraPE-PE.fa, while for the re…
Comment: cellranger error message by Max • 0
I think the problem is your fastq_id. This should also read "RabhiN_PHLGEX". Hope this helps!
Comment: How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK by Giulio Genovese ▴ 390
@yokofakun is correct. Also, do notice that the GATK option `--RECOVER_SWAPPED_REF_ALT True` does not work with indels. In general, if your…
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