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413 results • Page
4 of 9
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0
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1
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3.0k
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Tutorial:
Getting the lineage of an organism from NCBI taxonomy data
biosql
python
taxonomy
updated 14 months ago by
Ram
43k • written 5.8 years ago by
vimalkvn
▴ 320
77
votes
13
replies
16k
views
12 follow
Tutorial:
Exploring cancer mutation data portals
TCGA
Cancer
ICGC
Data-Portal
Mutation
updated 2.6 years ago by
Ram
43k • written 10.0 years ago by
Malachi Griffith
20k
6
votes
10
replies
5.3k
views
Tutorial:
Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR
dna-methylation
updated 14 months ago by
Ram
43k • written 6.2 years ago by
dec986
▴ 380
43
votes
6
replies
12k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl
maf
tcga
vcf
updated 14 months ago by
Ram
43k • written 10.3 years ago by
Cyriac Kandoth
6.1k
5
votes
3
replies
5.4k
views
Tutorial:
bam2rpkm by bedtools
bam
RNA-Seq
bedtools
rpkm
updated 14 months ago by
toxin08x
• 0 • written 6.6 years ago by
jmzeng1314
▴ 140
16
votes
11
replies
8.3k
views
Tutorial:
How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta
how-to
documentation
14 months ago by
Ram
43k
106
votes
6
replies
26k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 14 months ago by
Ram
43k • written 5.7 years ago by
finswimmer
16k
18
votes
40
replies
18k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 3.9 years ago by
krishdb38
• 0 • written 7.9 years ago by
Esaie
▴ 170
24
votes
4
replies
7.7k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
heatmap
chip-seq
atac-seq
EnrichedHeatmap
updated 14 months ago by
Ram
43k • written 4.8 years ago by
ATpoint
82k
15
votes
4
replies
4.6k
views
Tutorial:
RNASeq tutorial for gene differential expression analysis
Transcriptomics
bioconductor
RNA-Seq
R
updated 14 months ago by
Ram
43k • written 3.8 years ago by
Thind amarinder
▴ 340
26
votes
0
replies
2.5k
views
Tutorial:
Resources / databases for clinical interpretation of cancer variants
interpretation
cancer
annotation
variant
updated 14 months ago by
Ram
43k • written 4.6 years ago by
Malachi Griffith
20k
10
votes
1
reply
2.3k
views
Tutorial:
introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2
fastv
COVID-19
updated 14 months ago by
Ram
43k • written 4.1 years ago by
chen
★ 2.5k
60
votes
52
replies
44k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 14 months ago by
Ram
43k • written 7.6 years ago by
steve
★ 3.5k
13
votes
7
replies
6.3k
views
Tutorial:
STARsolo config for 10x Chromium v1, v2, v3
Chromium
10x
STARsolo
STAR
updated 14 months ago by
Ram
43k • written 3.7 years ago by
Kevin Blighe
88k
21
votes
26
replies
9.8k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 9 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.6k
0
votes
0
replies
1.1k
views
Tutorial:
BrainArray CDF, annotation, etc
db
brainarray
cdf
updated 14 months ago by
Ram
43k • written 3.7 years ago by
Kevin Blighe
88k
12
votes
0
replies
2.8k
views
Tutorial:
Long versus wide data for plotting genomics data in R.
ggplot2
tidyverse
data.table
R
updated 14 months ago by
Ram
43k • written 3.7 years ago by
rpolicastro
13k
1
vote
1
reply
1.4k
views
Tutorial:
Downloading GnuWin and using to convert txt to bed file for windows users
bed
bed2txt
sequencing
txt
updated 14 months ago by
Ram
43k • written 3.8 years ago by
opheevallee
• 0
4
votes
3
replies
4.6k
views
Tutorial:
How to get full taxonomy classification using taxize and myTAI
taxonomy
R
updated 14 months ago by
Ram
43k • written 6.1 years ago by
Daniel
★ 4.0k
4
votes
1
reply
1.4k
views
Tutorial:
Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED
BEDtools
updated 14 months ago by
Ram
43k • written 3.8 years ago by
sdsubaru33
▴ 40
3
votes
0
replies
3.7k
views
Tutorial:
Sorting GFF/GTF files
gtf
gff
updated 14 months ago by
Ram
43k • written 3.8 years ago by
Juke34
8.6k
20
votes
6
replies
5.7k
views
Tutorial:
Open Targets and programmatic access
open-targets
disease
API
drug
updated 14 months ago by
Ram
43k • written 7.7 years ago by
Denise CS
★ 5.2k
2
votes
2
replies
2.1k
views
Tutorial:
Human mitochondrial DNA annotation in SnpEff
chrMT
SNP
snpEff
updated 14 months ago by
Ram
43k • written 3.9 years ago by
Arup Ghosh
3.2k
12
votes
5
replies
2.5k
views
Tutorial:
FASTA file split
fasta
updated 14 months ago by
Ram
43k • written 3.9 years ago by
Juke34
8.6k
0
votes
0
replies
1.8k
views
Tutorial:
VIDEO: Installing BLAST Databases on Your Own Computer
BLAST-databases
Linux
sequence
MacOSX
updated 14 months ago by
Ram
43k • written 3.9 years ago by
brian.fristensky
▴ 460
0
votes
0
replies
1.0k
views
Tutorial:
VIDEO: BLAST Searches Through a Data Science Lens
Covid19
Data-Science
sequence
BLAST
updated 14 months ago by
Ram
43k • written 3.9 years ago by
brian.fristensky
▴ 460
2
votes
1
reply
1.6k
views
Tutorial:
A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2
fastv
COVID-19
viruses
updated 14 months ago by
Ram
43k • written 4.0 years ago by
chen
★ 2.5k
73
votes
27
replies
28k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 months ago by
snardeli
• 0 • written 10.3 years ago by
Istvan Albert
100k
59
votes
43
replies
21k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 14 months ago by
Ram
43k • written 6.7 years ago by
Rox
★ 1.4k
20
votes
7
replies
6.4k
views
Tutorial:
Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2
RNA-Seq
R
updated 14 months ago by
Ram
43k • written 5.6 years ago by
ahmad mousavi
▴ 800
4
votes
0
replies
1.8k
views
Tutorial:
NIH CDE browser for TCGA clinical data CDE codes
nih
tcga
metadata
cde
updated 14 months ago by
Ram
43k • written 4.1 years ago by
Kevin Blighe
88k
10
votes
4
replies
11k
views
Tutorial:
Using the MinION MinKNOW software on Ubuntu 1604
long-reads
oxford-nanopore
minion
updated 14 months ago by
Ram
43k • written 4.9 years ago by
colindaven
6.4k
0
votes
0
replies
1.3k
views
Tutorial:
Training GeneMark-EP+ ab-initio tool
abinitio
training
genemark
annotation
updated 14 months ago by
Ram
43k • written 4.3 years ago by
Juke34
8.6k
2
votes
1
reply
3.2k
views
Tutorial:
How to extract and filter SNP data from the genotyping-by-sequencing (GBS) data in vcf format using bcftools
bcftools
SNP-Filtering
VCF
updated 14 months ago by
Ram
43k • written 4.2 years ago by
Asad Prodhan
▴ 10
5
votes
0
replies
3.3k
views
Tutorial:
How to run CWL with Nextflow
cwl
nextflow
updated 14 months ago by
Ram
43k • written 4.2 years ago by
steve
★ 3.5k
5
votes
2
replies
2.3k
views
Tutorial:
Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA
closestBed
bedtools-closest
bedtools
updated 14 months ago by
Ram
43k • written 5.3 years ago by
linuxborg2
▴ 10
50
votes
3
replies
4.8k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 14 months ago by
Ram
43k • written 5.4 years ago by
ATpoint
82k
21
votes
9
replies
6.6k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
updated 14 months ago by
Ram
43k • written 10.9 years ago by
Medhat
9.7k
288
votes
39
replies
184k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 13 months ago by
Ram
43k • written 9.7 years ago by
Obi Griffith
20k
64
votes
26
replies
14k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 14 months ago by
Ram
43k • written 6.7 years ago by
Kevin Blighe
88k
34
votes
15
replies
6.6k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 14 months ago by
Ram
43k • written 4.9 years ago by
Shicheng Guo
★ 9.4k
20
votes
4
replies
2.7k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 14 months ago by
Ram
43k • written 5.0 years ago by
nim.1111.ou
▴ 180
15
votes
7
replies
6.5k
views
Tutorial:
Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq
peaks
R
HOMER
updated 14 months ago by
Ram
43k • written 8.0 years ago by
steve
★ 3.5k
2
votes
0
replies
4.7k
views
Tutorial:
Calculation of TSS Scores for ATAC-seq Data
next-gen-sequencing
updated 14 months ago by
Ram
43k • written 4.8 years ago by
Sael
▴ 20
0
votes
0
replies
1.1k
views
Tutorial:
Apply ALoFT to identify loss-of-function somatic or germline variants
ALoFT
updated 14 months ago by
Ram
43k • written 4.9 years ago by
Shicheng Guo
★ 9.4k
16
votes
11
replies
14k
views
7 follow
Tutorial:
retrieve full TCGA datasets from cBioportal with R
TCGA
RNA-seq
data-retrieval
cBioportal
R
updated 14 months ago by
Ram
43k • written 7.6 years ago by
TriS
★ 4.7k
10
votes
5
replies
24k
views
Tutorial:
Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 14 months ago by
Ram
43k • written 5.8 years ago by
Shicheng Guo
★ 9.4k
6
votes
3
replies
4.5k
views
Tutorial:
Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment
sequencing
RNA-seq
gene
updated 14 months ago by
Ram
43k • written 5.6 years ago by
contact
▴ 40
0
votes
0
replies
1.1k
views
Tutorial:
Introduction to Gen3 Webinar
gen3
open-source
data-commons
big-data
updated 14 months ago by
Ram
43k • written 5.3 years ago by
Danielle
▴ 310
0
votes
1
reply
1.4k
views
Tutorial:
SFA (Stochastic Frontier Analysis) Frontier 4.1
r
spss
updated 14 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
413 results • Page
4 of 9
Recent Votes
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
Comment: How does FindNeighbors() and FindClusters() related and work?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
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Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input?
by
Pierre Lindenbaum
161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem
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Pierre Lindenbaum
161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
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DGTool
▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
b.contreras.moreira
▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input?
by
LucisTheFather
• 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
thank you
Comment: How to extract cells of different species after mapping with combined genome?
by
Tony
• 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 20
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
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by
Nyksubuz
▴ 20
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
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by
Nyksubuz
▴ 20
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem
by
saifulislam99121
• 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
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