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143 results • Page
2 of 3
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3
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2
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Tutorial:
Galaxy Tutorial on ChIP-seq
galaxy
ChIP-Seq
updated 11 months ago by
Ram
43k • written 7.0 years ago by
anton
▴ 30
18
votes
2
replies
5.9k
views
Tutorial:
Update kraken databases
database
kraken
k-mer
python
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Sej Modha
5.3k
6
votes
2
replies
4.2k
views
Tutorial:
GATK method for filtering vcf lines using GT values at all or multisample level.
genome
vcf
genotype
variant-filtration
updated 11 months ago by
Ram
43k • written 6.9 years ago by
kirannbishwa01
★ 1.6k
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
3
votes
2
replies
2.7k
views
Tutorial:
Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences
Workshops
updated 11 months ago by
Ram
43k • written 7.0 years ago by
jnowacki
▴ 100
1
vote
2
replies
877
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
3
votes
2
replies
534
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
8
votes
2
replies
1.1k
views
Tutorial:
Updated List of Unix tutorials 2023
Unix
updated 8 months ago by
Ram
43k • written 8 months ago by
carlopecoraro2
★ 2.5k
1
vote
2
replies
1.5k
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
20
votes
2
replies
3.4k
views
Tutorial:
Beginner's Handbook to Next Generation Sequencing
NGS
updated 11 months ago by
Ram
43k • written 7.1 years ago by
support
▴ 650
3
votes
2
replies
8.8k
views
Tutorial:
Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ
UMI
fastp
updated 11 months ago by
Ram
43k • written 6.4 years ago by
chen
★ 2.5k
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
4 months ago by
GenoMax
141k
5
votes
2
replies
3.1k
views
Tutorial:
Get GC Content from UCSC with perl script (mysql)
myql
ucsc
gc-content
perl
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Shicheng Guo
★ 9.4k
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 6.6 years ago by
imlituan
▴ 110
0
votes
1
reply
3.2k
views
Tutorial:
Accessing sequences using batch entrez
genome
updated 11 months ago by
Ram
43k • written 6.5 years ago by
mawia.martha
• 0
0
votes
1
reply
288
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
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
1
vote
1
reply
328
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
1
reply
407
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
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 11 months ago by
Ram
43k • written 6.9 years ago by
kirannbishwa01
★ 1.6k
0
votes
1
reply
530
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
6
votes
1
reply
435
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
1
reply
1.9k
views
Tutorial:
Nonparametric Regression STATA 15
STATA-15
Nonparametric-Regression
STATA
updated 11 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
0
votes
1
reply
538
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
3
votes
1
reply
644
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
8.5k
15
votes
1
reply
7.1k
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
7
votes
1
reply
2.2k
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
3
votes
1
reply
3.4k
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
updated 11 weeks ago by
MaxF
▴ 120 • written 2.7 years ago by
Kevin Blighe
87k
0
votes
0
replies
651
views
Tutorial:
Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling
R
Computational-Biology
10 months ago by
sinha.shriprakash
▴ 20
2
votes
0
replies
709
views
Tutorial:
Get a list of genes associated with a drug in 1 min
drug
genes
drug-targets
updated 10 months ago by
Ram
43k • written 10 months ago by
Coremine Medical
▴ 20
1
vote
0
replies
2.6k
views
Tutorial:
GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo
R
data-mining
differential-gene-expression
RNA-Seq
updated 10 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
0
votes
0
replies
677
views
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
368
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 7.0 years ago by
Sachin Pundhir
▴ 100
0
votes
0
replies
664
views
Tutorial:
How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
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
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
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
1
vote
0
replies
246
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
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
0
votes
0
replies
243
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
817
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
737
views
Tutorial:
best practices for single-cell RNAseq analysis
cell
single
scRNAseq
10 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
274
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
5
votes
0
replies
1.6k
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 6.2 years ago by
Jeremy Leipzig
22k
1
vote
0
replies
607
views
Tutorial:
How to make a perfect heatmap using RNAseq data
heatmap
RNAseq
rstats
10 months ago by
Ming Tommy Tang
★ 3.9k
3
votes
0
replies
224
views
Tutorial:
Premade library preparation – considerations, tips and tricks (IA)
Premade-library
Illumina
NovaSeqX
8 weeks ago by
Novogene
▴ 420
2
votes
0
replies
405
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
143 results • Page
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Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
NGS forensics: how to know if data is fabricated
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How do I find out the read lenght of a fastq file?
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Comment: NGS forensics: how to know if data is fabricated
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noodle
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> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
Comment: ScRNAseq-How to correctly choose cell type marker genes
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Francesco
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Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated
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noodle
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> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated
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ATpoint
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My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated
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This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
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It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
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[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
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3.2k
Use the standalone version of Nextflow and specify the process-specific conda environments paths.
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Jeremy Leipzig
22k
can you show us an exonic position in your VCF file that is all `./.`?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
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O.rka
▴ 710
Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
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by
colindaven
6.4k
I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
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Istvan Albert
100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
Comment: ScRNA data question
by
starswillfade
▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling
by
zihanss
• 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
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