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141 results • Page
3 of 3
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0
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684
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Tutorial:
T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq
TCR
single-cell
computational
biology
8 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
375
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
5 months ago by
rohitsatyam102
▴ 850
4
votes
0
replies
2.3k
views
Tutorial:
Accurate prediction of active enhancers using PARE
ChIP-Seq
histone-modification
enhancer
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Sachin Pundhir
▴ 100
1
vote
0
replies
350
views
Tutorial:
4 CITE-seq tutorials
CTIE-seq
4 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
226
views
Tutorial:
Parsing HMMER output
HMMER
updated 6 weeks ago by
GenoMax
142k • written 6 weeks ago by
I0110
▴ 140
2
votes
0
replies
3.2k
views
Tutorial:
How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix
Seurat
single-cell
rstats
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
196
views
Tutorial:
DNA Methylation: Sequencing Techniques
WGBS
RRBS
15 days ago by
Novogene
▴ 420
0
votes
0
replies
1.6k
views
Tutorial:
PLS SEM (Partial Least Square Sructural Equation Modeling) Analysis WarpPLS 6
R
updated 11 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
1
vote
0
replies
255
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
2
votes
0
replies
1.2k
views
Tutorial:
GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo
R
data-mining
Gene-pathway-enrichment
RNA-Seq
updated 10 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
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
2
votes
0
replies
416
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
2
votes
0
replies
481
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
0
votes
0
replies
1.4k
views
Tutorial:
Data Panel In R Commander
R
updated 11 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
1
vote
0
replies
690
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
0
votes
0
replies
252
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
1
vote
0
replies
825
views
Tutorial:
List of Machine Learning-Based Scoring Function Papers
machine-learning
docking
papers
updated 5 months ago by
Ram
43k • written 13 months ago by
Milad
▴ 10
3
votes
0
replies
745
views
Tutorial:
best practices for single-cell RNAseq analysis
cell
single
scRNAseq
10 months ago by
Ming Tommy Tang
★ 3.9k
5
votes
0
replies
1.7k
views
Tutorial:
GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo
RNA-Seq
data-mining
SRA
updated 10 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
3
votes
0
replies
2.2k
views
Tutorial:
Deep Learning for Cancer Immunotherapy
keras
tensorflow
updated 11 months ago by
Ram
43k • written 6.3 years ago by
Jeremy Leipzig
22k
1
vote
0
replies
613
views
Tutorial:
How to make a perfect heatmap using RNAseq data
heatmap
RNAseq
rstats
10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
374
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
0
votes
0
replies
2.2k
views
Tutorial:
Transforming (Transformation) Data LN, Log, SQRT In R Commander
R
updated 11 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
1
vote
0
replies
289
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
1
vote
0
replies
333
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
4 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
349
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
6
votes
0
replies
541
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
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
2.9k
views
Tutorial:
Autocorrelation With Breusch Godfrey Serial Correlation LM Test R Commander
LM-Test
R
Autocorrelation
Breusch-Godfrey
updated 11 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
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
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
1
vote
0
replies
285
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
2
votes
0
replies
3.3k
views
Tutorial:
use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene
slicer
fastq
splitter
updated 10 months ago by
Ram
43k • written 6.5 years ago by
chen
★ 2.5k
0
votes
0
replies
325
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
0
replies
525
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
1
vote
0
replies
640
views
Tutorial:
common mistakes in using spreadsheets
excel
spreadsheet
structured-data
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
1.4k
views
Tutorial:
Fall 2017 Introduction to Human Genomics for Clinical Informaticists
genome
updated 11 months ago by
Ram
43k • written 6.3 years ago by
bdolin
▴ 90
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
5
votes
0
replies
2.2k
views
Tutorial:
Installing multiprocessor-capable MEME to work with a Slurm job scheduler environment
slurm
meme
parallel
updated 11 months ago by
Ram
43k • written 6.6 years ago by
Alex Reynolds
35k
0
votes
0
replies
471
views
Tutorial:
Using easyPubMed and scholar package to get all citations of your paper
scholar
easyPubMed
6 months ago by
rohitsatyam102
▴ 850
0
votes
0
replies
257
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
141 results • Page
3 of 3
Recent Votes
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
Answer: Does comparing two different groups to a common third group introduce bias in th
Comment: High Malat-1 expression in single cell data
Comment: High Malat-1 expression in single cell data
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Recent Awards •
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Scholar
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GenoMax
142k
Popular Question
to
curious
▴ 750
Popular Question
to
M.
▴ 30
Student
to
carolofharvest
▴ 30
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e.r.zakiev
▴ 210
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dsull
★ 6.0k
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eebloom
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Recent Replies
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme
by
e.r.zakiev
▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ
by
GenoMax
142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
Comment: Raw counts using stringtie
by
GenoMax
142k
> Error parsing strand from GFF line Looking at this error and the listing of files in your directory it looks like you need to `gunzip` t…
Comment: High Malat-1 expression in single cell data
by
dsull
★ 6.0k
I briefly looked at those genes on a genome browser -- there are a lot of repeat elements in those genes, meaning a lot of counts assigned …
Comment: High Malat-1 expression in single cell data
by
carolofharvest
▴ 30
Thank you for sharing. What are your thoughts on the genes Gm42418, AY036118, and Gm26917? Some articles suggest that clusters with an abu…
Comment: Do I need to go back and filter my long-reads?
by
GenoMax
142k
> I think I will filter the reads ultimately. If your data was not run and basecalled using the same exact version of pore/software for a…
Comment: Raw counts using stringtie
by
Ram
43k
What is `stringie.sh`? Try `./stringtie.sh -h` and then `more stringtie.sh`.
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