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412 results • Page
1 of 9
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5
votes
1
reply
98
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 13 hours ago by
dariober
14k • written 13 hours ago by
nhaus
▴ 340
5
votes
5
replies
601
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 12 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
12 days ago by
Kevin Blighe
87k
5
votes
13
replies
1.6k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 17 days ago by
ATpoint
82k • written 18 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 18 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
1
vote
0
replies
201
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
19 days ago by
Novogene
▴ 420
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 19 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
233
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
219
views
Tutorial:
Premade library preparation – considerations, tips and tricks (II)
Illumina.
Premade-library.
NovaSeqX.
10 weeks ago by
Novogene
▴ 420
3
votes
0
replies
237
views
Tutorial:
Premade library preparation – considerations, tips and tricks (IA)
Premade-library
Illumina
NovaSeqX
10 weeks ago by
Novogene
▴ 420
6
votes
0
replies
551
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
327
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
637
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
554
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
434
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
301
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
254
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
264
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
292
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
286
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
356
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
253
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
293
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
333
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
558
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
418
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
261
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
346
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
608
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
458
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
269
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
354
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
378
views
Tutorial:
download metadata using GEOquery
computational-biology
GEO
metadata
updated 4 months ago by
Ram
43k • written 4 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
337
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
5 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
379
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
476
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
748
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
529
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
575
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
543
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
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Answer: HCL database download
Answer: Tissue-specific DEG analysis with DEseq2
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Answer: TFs and Gene databases
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Answer: HCL database download
by
sooni
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I solved the problem by conneting another internet exploer. I think it was probably a problem with Chrome itself.
Answer: barcode of TCR-sequencing
by
mizraelson
▴ 60
Hi, What protocol did you use for TCR-seq library preparation? Generally speaking, there is no need to remove barcodes, as MiXCR can work …
Comment: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C
by
qwertyuiop26
• 0
I've implemented fm index with backward search and need an inexact search to implement on FM index, I couldn't understand how fm index coul…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 400
The md5 hash they refer to on line 22 (f46a7ca244afef522b22a11bd33d27b1) appears to map to a *S. aureus* strain, not *S. hominis* (you can …
Comment: Correlating Bulk Differential Expression with quantitative
by
Qroid
▴ 40
You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bio…
Comment: Help with generating annotation database for dog genome to use in ANNOVAR for v
by
sainavyav22
• 0
Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
Answer: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Jeremy Leipzig
22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases
by
jared.andrews07
★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
GenoMax
142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help
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