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141 results • Page
2 of 3
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Votes
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20
votes
2
replies
3.4k
views
Tutorial:
Beginner's Handbook to Next Generation Sequencing
NGS
updated 12 months ago by
Ram
43k • written 7.1 years ago by
support
▴ 650
3
votes
2
replies
3.9k
views
Tutorial:
Galaxy Tutorial on ChIP-seq
galaxy
ChIP-Seq
updated 12 months ago by
Ram
43k • written 7.1 years ago by
anton
▴ 30
18
votes
2
replies
5.9k
views
Tutorial:
Update kraken databases
database
kraken
k-mer
python
updated 12 months ago by
Ram
43k • written 7.0 years ago by
Sej Modha
5.3k
7
votes
2
replies
1.9k
views
Tutorial:
Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by
Ram
43k • written 6.7 years ago by
bdolin
▴ 90
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
ATpoint
82k • written 3 months ago by
Julia Ma
▴ 120
4
votes
2
replies
1.1k
views
Tutorial:
How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC
transcription
factor
ChIP-seq
9 months ago by
Ming Tommy Tang
★ 3.9k
10
votes
2
replies
3.7k
views
Tutorial:
Graph visualization with igraph in R
Visualization
igraph
Graph
R
Network
updated 12 months ago by
Ram
43k • written 7.1 years ago by
Jean-Karim Heriche
27k
1
vote
2
replies
1.6k
views
Tutorial:
ViennaRNA package installation in Windows
windows
rna
mfold
viennarna
updated 10 months ago by
Ram
43k • written 19 months ago by
Sandhiya
▴ 20
4
votes
2
replies
2.9k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 8 months ago by
GenoMax
142k • written 4.0 years ago by
ATpoint
82k
1
vote
2
replies
891
views
Tutorial:
How to ask computational biology questions
computational-biology
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
6
votes
2
replies
5.0k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
5 months ago by
GenoMax
142k
0
votes
1
reply
3.2k
views
Tutorial:
Accessing sequences using batch entrez
genome
updated 11 months ago by
Ram
43k • written 6.6 years ago by
mawia.martha
• 0
3
votes
1
reply
3.4k
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
updated 3 months ago by
MaxF
▴ 120 • written 2.8 years ago by
Kevin Blighe
87k
0
votes
1
reply
1.9k
views
Tutorial:
Nonparametric Regression STATA 15
STATA-15
Nonparametric-Regression
STATA
updated 11 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
6
votes
1
reply
469
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis
differential-expression
RNA-seq
updated 3 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 120
0
votes
1
reply
549
views
Tutorial:
TAPIS installation and usage
APA
Iso-seq
splicing
TAPIS
analysis
alternative
updated 8 months ago by
ATpoint
82k • written 8 months ago by
JC
▴ 30
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
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
10
votes
1
reply
9.3k
views
Tutorial:
How to select reads with specific flag using samtools
next-gen-sequencing
updated 11 months ago by
Ram
43k • written 6.7 years ago by
imlituan
▴ 110
1
vote
1
reply
358
views
Tutorial:
Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING
ppi
updated 3 months ago by
Ram
43k • written 4 months ago by
Julia Ma
▴ 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
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
3
votes
1
reply
652
views
Tutorial:
Coordinate Systems and genomic variant description
coordinate-system
HGVS
normalization
VCF
updated 9 months ago by
Ram
43k • written 9 months ago by
Juke34
8.6k
4
votes
1
reply
1.9k
views
Tutorial:
One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.7 years ago by
maleknias
▴ 40
7
votes
1
reply
2.3k
views
Tutorial:
A gentle introduction to biogo
sequence
golang
biogo
updated 11 months ago by
Ram
43k • written 6.5 years ago by
Botond Sipos
★ 1.7k
7
votes
1
reply
153
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 2 days ago by
dariober
14k • written 2 days ago by
nhaus
▴ 360
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
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
15
votes
1
reply
7.2k
views
Tutorial:
A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl
SAM
blast
BED
updated 11 months ago by
Ram
43k • written 6.5 years ago by
Joseph Hughes
★ 3.0k
3
votes
1
reply
2.3k
views
Tutorial:
Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools
bam
alignment
fastq
sequence
updated 12 months ago by
Ram
43k • written 6.9 years ago by
kirannbishwa01
★ 1.6k
0
votes
0
replies
8.1k
views
Tutorial:
Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R
eviews
updated 11 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
2
votes
0
replies
1.4k
views
Tutorial:
Principal Component Analysis (PCA ON T-BIOINFO)
RNA-Seq
next-gen
updated 11 months ago by
Ram
43k • written 5.9 years ago by
elia.brodsky
▴ 340
2
votes
0
replies
6.9k
views
Tutorial:
How to - Install Python packages in a virtual environment (virtualenv)
ubuntu
cutadapt
virtualenv
python
windows
updated 11 months ago by
Ram
43k • written 6.4 years ago by
vimalkvn
▴ 320
2
votes
0
replies
482
views
Tutorial:
Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering
gene-expression
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
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
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
1
vote
0
replies
297
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
3.1k
views
Tutorial:
Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test
R-Commander
updated 11 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
0
votes
0
replies
1.3k
views
Tutorial:
In the cloud - Guide to running VerifyBamID to estimate DNA sample contamination
sequence
cloud
dna
sequencing
updated 11 months ago by
Ram
43k • written 5.8 years ago by
corlinp
• 0
0
votes
0
replies
3.6k
views
Tutorial:
SFA (Stochastic Frontier Analysis) STATA 14
R
updated 11 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
1
vote
0
replies
361
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
2
votes
0
replies
2.1k
views
Tutorial:
How to display Agilent CGH array in IGV
IGV
CGH
updated 11 months ago by
Ram
43k • written 6.4 years ago by
sacha
★ 2.4k
0
votes
0
replies
388
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
2
votes
0
replies
724
views
Tutorial:
Get a list of genes associated with a drug in 1 min
drug
genes
drug-targets
updated 11 months ago by
Ram
43k • written 11 months ago by
Coremine Medical
▴ 20
1
vote
0
replies
692
views
Tutorial:
How to convert gene ids in R
computational-biology
gene-id
rstats
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
2
votes
0
replies
1.5k
views
Tutorial:
Webinar: Extracting research evidence from publications
text-mining
ontology
pubmed
updated 11 months ago by
Ram
43k • written 6.2 years ago by
Maria_Levchenko
▴ 60
0
votes
0
replies
243
views
Tutorial:
Parsing HMMER output
HMMER
updated 6 weeks ago by
GenoMax
142k • written 6 weeks ago by
I0110
▴ 140
2
votes
0
replies
1.2k
views
Tutorial:
Analysis of Smart-Seq3 data with kallisto-bustools
single-cell
kallisto
transcriptomics
smart-seq3
pipeline
updated 5 months ago by
Ali
• 0 • written 15 months ago by
firestar
★ 1.6k
1
vote
0
replies
207
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
21 days ago by
Novogene
▴ 420
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
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
1
vote
0
replies
344
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
5 months ago by
Ming Tommy Tang
★ 3.9k
7
votes
0
replies
602
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
8 months ago by
barslmn
★ 2.1k
1
vote
0
replies
693
views
Tutorial:
How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix
scRNA-seq
single-cell
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
1.7k
views
Tutorial:
Using Subversion to update /devel branch of Bioconductor package
bioconductor
subversion
updated 12 months ago by
Ram
43k • written 6.8 years ago by
Bohdan Khomtchouk
▴ 350
141 results • Page
2 of 3
Recent Votes
Answer: Nextflow: how to get the process work dir, within the process
use firehose_get to download TCGA data
Download data from TCGA
Comment: Importing a fastq file
EdgeR - relationship between logFC and coefficients
Answer: EdgeR - relationship between logFC and coefficients
Detecting highly variable genes within replicates
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Answer: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
• 0
Thank you for the information.
Comment: LncRNA Nomenclature
by
jain72744
▴ 10
My data is based on gene counts and the respective gene IDs are given so I should work with ENSGs? lncRNA_transcripts <- getBM(attributes …
Answer: DESeq2 error
by
ATpoint
82k
At least one group needs replication. That is the short answer. For a longer answer add details on experimental design.
Comment: When should I use R-MarkDown over R-Script ?
by
ATpoint
82k
Why particular question? Rmarkdown is a composite of markdown and code. You can nicely separate free text, explanation, comments etc. from…
Comment: LncRNA Nomenclature
by
ATpoint
82k
RNA-seq is typically analyzed on gene rather than transcript level. Are your counts gene or transcript?
Comment: EdgeR - relationship between logFC and coefficients
by
gBioStar5
▴ 10
Thanks a lot, this was very helpful. I'll keep that in mind.
Answer: EdgeR - relationship between logFC and coefficients
by
Gordon Smyth
★ 7.1k
Results presented by topTags() are on the log2 scale. Coefficients stored internally in the DGELRT object are on the loge scale. If you con…
Answer: Importing a fastq file
by
size_t
▴ 120
run command `explorer.exe .` in wsl terminal, and then drag file to folder
Comment: Contig assembly task, errors
by
Philipp Bayer
8.4k
Hi Ricardo! CAP3 is an 'older' overlap assembler from 1999 which is perfectly suited for these kinds of 'small' tasks. I used it last in my…
Comment: absolute path for symbolic links in Snakefile
by
Jesse
▴ 770
That's really handy, and much more of a general solution than stripping off the directory names! So yifangt86, if you're on Linux you can …
Comment: Truncated metadata file report from ENA Portal API
by
GenoMax
142k
Are you missing a `"` at the end of the URL. Doing wget -O test.out "https://www.ebi.ac.uk/ena/portal/api/filereport?accession=PRJNA43…
Comment: Different output for read length
by
marco.barr
▴ 100
very strange, I double checked the BAM file and it is the same one I used for your request. Are the commands I wrote above correct? How is …
Comment: Different output for read length
by
Pierre Lindenbaum
161k
the first read as a length of 1747, i wonder how you can just find '50' $ wget -qO - "https://gist.githubusercontent.com/Macdot3/4650…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
bk11
★ 2.4k
Yes, `CreateAssayObject` function is used for only expression matrix.
Comment: Different output for read length
by
marco.barr
▴ 100
Here is my result, I hope you can see it. [https://gist.github.com/Macdot3/4650243a10540d8c06f728ffc16a136c][1] [1]: https://gist.gith…
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