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412 results • Page
1 of 9
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Rank
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Replies
6
votes
1
reply
126
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 1 day ago by
dariober
14k • written 1 day ago by
nhaus
▴ 350
5
votes
5
replies
607
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 4 days ago by
Mbofire
• 0 • written 13 days ago by
Ming Tommy Tang
★ 3.9k
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
13 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 18 days ago by
ATpoint
82k • written 19 days ago by
BioinfGuru
★ 1.7k
7
votes
3
replies
2.9k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 19 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
1
vote
0
replies
202
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
20 days ago by
Novogene
▴ 420
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 20 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
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 5 weeks ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
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
Ram
43k • written 6.2 years ago by
Kevin Blighe
87k
0
votes
0
replies
235
views
Tutorial:
Parsing HMMER output
HMMER
updated 6 weeks ago by
GenoMax
142k • written 6 weeks ago by
I0110
▴ 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
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 7 weeks ago by
jkbonfield
★ 1.2k • written 5.2 years ago by
finswimmer
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
Konstantinos
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
2
votes
0
replies
221
views
Tutorial:
Premade library preparation – considerations, tips and tricks (II)
Illumina.
Premade-library.
NovaSeqX.
10 weeks ago by
Novogene
▴ 420
3
votes
0
replies
239
views
Tutorial:
Premade library preparation – considerations, tips and tricks (IA)
Premade-library
Illumina
NovaSeqX
10 weeks ago by
Novogene
▴ 420
6
votes
0
replies
554
views
Tutorial:
12 useful command line tools and tricks for genomics data science
unix
updated 3 months ago by
zx8754
11k • written 3 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
328
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
638
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq
TOSICA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
3
votes
2
replies
556
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by
ATpoint
82k • written 3 months ago by
Julia Ma
▴ 120
2
votes
1
reply
438
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq
space
clustering
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
1
reply
304
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq
MetaTiME
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
0
replies
256
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-3
scRNA-seq
SCSA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
0
replies
266
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA-2
scRNA-seq
SCSA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
1
vote
0
replies
294
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype auto annotation with SCSA
scRNA-seq
SCSA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
0
replies
288
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-3
scRNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
1
vote
0
replies
357
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction
scRNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
0
replies
255
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
294
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
335
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-2
scRNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
1
reply
559
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
2
votes
0
replies
420
views
Tutorial:
Bulk RNA-seq: WGCNA (Weighted gene co-expression network analysis) analysis
WGCNA
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
1
vote
0
replies
262
views
Tutorial:
Bulk RNA-seq: TCGA database preprocess
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
1
vote
1
reply
350
views
Tutorial:
Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING
ppi
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
2
votes
3
replies
614
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis with DEseq2
python
pyDESeq2
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
6
votes
1
reply
463
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis
differential-expression
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
0
votes
0
replies
270
views
Tutorial:
Bulk RNA-seq: Batch correction in Bulk RNA-seq or microarray data
python
RNA-seq
batch-correction
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 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
GenoMax
142k • written 3.7 years ago by
lavinia.gordon
▴ 160
1
vote
0
replies
357
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
sil_bioinfo
▴ 40 • written 8 months ago by
Ming Tommy Tang
★ 3.9k
16
votes
3
replies
4.4k
views
Tutorial:
Methylation Analysis Tutorial in R_part2
cancer
methylation
RNA-Seq
R
updated 3.2 years ago by
zhuanggj706
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
0
votes
0
replies
380
views
Tutorial:
download metadata using GEOquery
computational-biology
GEO
metadata
updated 4 months ago by
Ram
43k • written 5 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
339
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
5 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
381
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
479
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
751
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 6 months ago by
Ram
43k • written 10.6 years ago by
Irsan
★ 7.8k
1
vote
0
replies
530
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
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
2
votes
0
replies
576
views
Tutorial:
Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf
sparql
data-management
graph
updated 7 months ago by
Ram
43k • written 7 months ago by
Pierre Lindenbaum
161k
0
votes
1
reply
544
views
Tutorial:
TAPIS installation and usage
APA
Iso-seq
splicing
TAPIS
analysis
alternative
updated 7 months ago by
ATpoint
82k • written 7 months ago by
JC
▴ 30
412 results • Page
1 of 9
Recent Votes
Answer: Why is RNA-Seq library size not constant among samples?
Answer: TFs and Gene databases
Answer: java out of memory error through beagle for imutation
A: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
Comment: Microarray pbrobe ID to gene ID problem
Answer: Microarray pbrobe ID to gene ID problem
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Comment: RNA seq analysis
by
prifa
• 0
thank you for your reply Zepper, a bit clarification, I took all the samples from SRA data table, but yes from different lab and also diffe…
Answer: How can I analysis Nomalized expression data?
by
christopher medway
▴ 460
A few options are described in this post https://support.bioconductor.org/p/9141424/
Comment: RNA seq analysis
by
Matthias Zepper
4.6k
That you have a varying number of replicates is not ideal ([see here why][1]), but manageable. See for example the [Specific experimental d…
Comment: Percentage coverage of reference genome by de novo genome
by
Joe
21k
OK, in that case it should be even easier as its just a single pairwise alignment, so the same advice holds.
Comment: FarmCPU - how to explain the reported 'effect'?
by
chloek88
• 0
Hi Phillip, Did you ever figure out the answer to this? I also have rMVP results with a column 'effect', values ranging from ~-1.4 to +1…
Comment: Soft-clipping read ends based on read group
by
chenl
▴ 10
Hi, Can you please share how did you clip both ends of the reads with ClipReads? Clipping form the start with `-CT "1-3"` for instance wor…
Comment: Phasing a mixture of two individuals' DNA with long reads
by
njornet
▴ 20
This is related to that other question but for now, the only thing I'm interested in is separating the three unique chromosomes, without as…
Comment: A question about reference genome for creating the consensus sequence
by
GenoMax
142k
> I wonder how to adjust the base genome. If you are looking to make changes to the reference you used for alignment then look into http…
Comment: Phasing a mixture of two individuals' DNA with long reads
by
GenoMax
142k
We had a related discussion in a prior thread by OP: https://www.biostars.org/p/9593780/ Do you have genotype (or independent sequence) da…
Answer: TFs and Gene databases
by
b.contreras.moreira
▴ 180
I can also suggest <https://footprintdb.eead.csic.es> which links TFs to their DNA motifs, not their gene targets.
Comment: Correlation Analysis
by
manaswwm
▴ 510
How many methylation and expression values do you have per gene? If per gene you have a table named - *gene_corr*; which has two columns - …
Comment: How do I change the title font size in ViolinPlot (Seurat)
by
Assa Yeroslaviz
★ 1.8k
thx for the explanation. I did look at the function and I also read in the help page, that you get a patchwork object, only when using `co…
Comment: Percentage coverage of reference genome by de novo genome
by
Lemonhope
• 0
Thank you, I'll check out Quast!
Answer: How do I change the title font size in ViolinPlot (Seurat)
by
ATpoint
82k
Looking at the source code of the function it seems that they make individual plots with ggplot when `features` is `> 1` and then use patch…
Comment: Percentage coverage of reference genome by de novo genome
by
Lemonhope
• 0
Thank you for the response to answer you question, no, the ddRADseq data (short paired end illumina reads) for all the samples were used …
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