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515 results • Page
2 of 11
Sort: Views
Rank
Views
Votes
Replies
19
votes
14
replies
8.2k
views
7 follow
Tool:
AfterQC: Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
PolyG
Quality-Control
Filtering
Fastq
AfterQC
updated 11 months ago by
Ram
44k • written 8.0 years ago by
chen
★ 2.5k
4
votes
0
replies
8.2k
views
Tool:
Snprelate: A Toolset For Relatedness And Principal Component Analysis Of Snp Data
parallel
pca
r
updated 11 months ago by
Ram
44k • written 11.3 years ago by
zx8754
11k
19
votes
5
replies
8.0k
views
Tool:
deepTools: user-friendly tools for the normalization and visualization of deep-sequencing data
Visualisation
RNA-Seq
QC
ChIP-Seq
updated 11 months ago by
Ram
44k • written 10.0 years ago by
Björn
▴ 670
3
votes
1
reply
8.0k
views
Tool:
New ultrafast interval tree implementation for Python: kerneltree
Interval-tree
Python
updated 11 months ago by
Ram
44k • written 6.1 years ago by
endrebak
▴ 960
0
votes
2
replies
7.9k
views
Tool:
The script to install the required packages for gene expression analysis using DESeq2 for downstream analysis and visualization
R
RNAseq
installation
DESeq2
9 months ago by
Aditya naman
• 0
14
votes
10
replies
7.9k
views
Tool:
ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
ReactomePA
R
Visualization
Pathway
Bioconductor
updated 11 months ago by
Ram
44k • written 7.9 years ago by
Guangchuang Yu
★ 2.6k
12
votes
9
replies
7.8k
views
Tool:
gogadget: an R package for go analysis visualization and interpretation
goseq
R
RNA-Seq
gogadget
updated 11 months ago by
Ram
44k • written 7.8 years ago by
Benn
8.3k
19
votes
4
replies
7.7k
views
Tool:
NanoPack: Scripts for long read sequencing data processing and analysis: NanoPlot, NanoFilt, NanoStat, NanoLyse, NanoComp
pacbio
long-reads
oxford-nanopore
updated 11 months ago by
Ram
44k • written 6.7 years ago by
WouterDeCoster
47k
16
votes
16
replies
7.7k
views
6 follow
Tool:
Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data
annotation
fusion
rna-seq
ngs
updated 11 months ago by
Ram
44k • written 10.7 years ago by
mikhail.shugay
3.5k
3
votes
1
reply
7.5k
views
Tool:
Weeder 2.0 - motif discovery tool updated
motif-discovery
chip-seq
weeder
updated 11 months ago by
Ram
44k • written 9.6 years ago by
Ian
6.0k
10
votes
1
reply
7.5k
views
Tool:
Comb-P: Combining Spatially Correlated P-Values
methylation
updated 11 months ago by
Ram
44k • written 11.6 years ago by
brentp
24k
13
votes
2
replies
7.4k
views
Tool:
Software For Detecting Differential Abundance In Meta-Genomic Samples
metagenomics
updated 11 months ago by
Ram
44k • written 11.6 years ago by
Istvan Albert
100k
20
votes
23
replies
7.3k
views
6 follow
Tool:
EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
easeq
Windows
Visualization
ChIP-Seq
updated 11 months ago by
Ram
44k • written 8.1 years ago by
Mads Lerdrup
▴ 460
4
votes
3
replies
7.3k
views
Tool:
Deindexer - A Standalone Demultiplexing Tool For Illumina Platform
illumina
updated 11 months ago by
Ram
44k • written 11.3 years ago by
jingtao09
▴ 110
15
votes
6
replies
7.2k
views
Tool:
Sambamba: High Performance Alternative For Samtools And Picard For Indexing, Sorting And Merging Bam Files
sambamba
bam
samtools
updated 11 months ago by
Ram
44k • written 10.7 years ago by
William
★ 5.3k
6
votes
3
replies
7.2k
views
Tool:
BioCircos.R: create shiny-friendly interactive multi-track circular plots in R
circos
R
htmlwidgets
shiny
updated 11 months ago by
Ram
44k • written 6.4 years ago by
lvulliard
▴ 60
11
votes
2
replies
7.1k
views
Tool:
fastp (the ultra-fast all-in-one FASTQ preprocessing tool) v0.18.0 released, 2X faster, with many new features.
fastp
QC
updated 11 months ago by
Ram
44k • written 5.9 years ago by
chen
★ 2.5k
5
votes
8
replies
7.1k
views
6 follow
Tool:
Converting MUMmer snps file to a real VCF file
VCF
mummer
SNP
updated 11 months ago by
Ram
44k • written 4.8 years ago by
Matteo Schiavinato
★ 3.6k
9
votes
1
reply
7.0k
views
Tool:
Rsem: Accurate Transcript Quantification From Rna-Seq Data With Or Without A Reference Genome
rna-seq
RSEM
updated 11 months ago by
Ram
44k • written 11.7 years ago by
Istvan Albert
100k
1
vote
4
replies
6.8k
views
Tool:
Jellyfish - Fast, Parallel K-Mer Counting For Dna
jellyfish
updated 11 months ago by
Ram
44k • written 12.0 years ago by
Istvan Albert
100k
3
votes
2
replies
6.6k
views
Tool:
Ancestry: AngularJS module with interactive lineage chart components based on D3.js
visualization
updated 11 months ago by
Ram
44k • written 7.9 years ago by
Lars Schöning
▴ 90
5
votes
1
reply
6.6k
views
Tool:
Trim Adapters Of Paired-End Reads (Fastq)
paired-end
adaptor-trimming
ngs
updated 11 months ago by
Ram
44k • written 11.3 years ago by
David Langenberger
11k
22
votes
8
replies
6.6k
views
Tool:
BioTuring Browser: Making single-cell sequencing data in published studies really accessible!
scRNA-Seq
single-cell
updated 11 months ago by
Ram
44k • written 5.7 years ago by
sonpham
▴ 580
13
votes
1
reply
6.6k
views
Tool:
clusterProfiler: an R package for comparing biological themes among gene clusters
GO
clusterProfiler
KEGG
R
GSEA
updated 11 months ago by
Ram
44k • written 7.9 years ago by
Guangchuang Yu
★ 2.6k
7
votes
6
replies
6.5k
views
Tool:
PlantTFDB and PlantRegMap: Plant Transcription Factor Database and Plant Regulation Data and Analysis Platform
transcriptional-regulation
enrichment
binding-site
updated 11 months ago by
Ram
44k • written 7.6 years ago by
jin
▴ 80
10
votes
3
replies
6.3k
views
Tool:
GenVisR: Genomic Visualizations in R
visualization
genomic
RNA-Seq
genvisr
updated 11 months ago by
Ram
44k • written 7.9 years ago by
Obi Griffith
20k
3
votes
8
replies
6.3k
views
Tool:
MFEprimer-2.0: A Fast Thermodynamics-Based Program For Checking Pcr Primer Specificity
primer
pcr
updated 11 months ago by
Ram
44k • written 12.0 years ago by
Wubin Qu
▴ 170
13
votes
14
replies
6.2k
views
9 follow
Tool:
open-cravat: variant annotation tool
open-cravat
updated 11 months ago by
Ram
44k • written 5.4 years ago by
slcrick
▴ 260
12
votes
5
replies
6.2k
views
Tool:
AGAT - Another Gff/Gtf Analysis Toolkit
gff
gtf
updated 11 months ago by
Ram
44k • written 4.4 years ago by
Juke34
8.6k
2
votes
5
replies
6.1k
views
Tool:
umitools - working with UMI incorporated data
UMI
sequencing
updated 11 months ago by
Ram
44k • written 9.9 years ago by
Joe Brown
▴ 70
17
votes
9
replies
6.1k
views
Tool:
Pathomx: Metabolic Pathway Visualisation And Analysis
python
pathway-visualization
updated 11 months ago by
Ram
44k • written 11.1 years ago by
Martin Fitzpatrick
▴ 180
19
votes
9
replies
6.1k
views
Tool:
Rlsim, A Package For Simulating Rna-Seq Library Preparation With Parameter Estimation
simulation
rna-seq
pcr
illumina
updated 11 months ago by
Ram
44k • written 11.1 years ago by
Botond Sipos
★ 1.7k
18
votes
2
replies
6.1k
views
Tool:
vcfanno quickly annotate a vcf with other VCFs, BEDs, BAMs
VCF
variant-annotation
updated 11 months ago by
Ram
44k • written 8.9 years ago by
brentp
24k
27
votes
13
replies
6.0k
views
Tool:
DEA.R: Command line script for differential expression analysis with R packages (DESeq2/edgeR/limma-voom)
edgeR
DESeq2
limma
RNA-Seq
updated 11 months ago by
Ram
44k • written 7.8 years ago by
WouterDeCoster
47k
9
votes
4
replies
6.0k
views
Tool:
BPGA - Bacterial Pan Genome Analysis pipeline
sequence
genome
comparative-genomics
bacteria
updated 11 months ago by
Ram
44k • written 8.0 years ago by
bpgatool
▴ 80
8
votes
6
replies
5.9k
views
Tool:
chromoMap- R package for Interactive visualization and Annotation of chromosomes or regions of any living organism.
annotation
R
genome
visualization
updated 11 months ago by
Ram
44k • written 5.1 years ago by
lakshayanand15
▴ 80
10
votes
0
replies
5.8k
views
Tool:
Shell utilities for QC of FASTQ/FASTA files (based on perl one-liners)
PERL
GNUPLOT
FASTA
FASTQ
FastQC
updated 11 months ago by
Ram
44k • written 10.1 years ago by
umer.zeeshan.ijaz
★ 1.8k
4
votes
3
replies
5.8k
views
Tool:
KeggExp: a web server for visualizing KEGG pathways maps when analyzing expression profile data
expression-profile-data
pathway-visualization
10 months ago by
liux.bio
▴ 360
10
votes
6
replies
5.7k
views
Tool:
Shell script to automate trimmomatic for multiple samples
bash
shell
trimmomatic
updated 11 months ago by
Ram
44k • written 5.0 years ago by
lakhujanivijay
5.8k
6
votes
0
replies
5.6k
views
Tool:
cnv_facets: somatic Copy Number Variant calling using the facets package
CNV
somatic
facets
cancer
updated 11 months ago by
Ram
44k • written 5.4 years ago by
dariober
14k
7
votes
5
replies
5.6k
views
Tool:
XENA: a new tool for cancer researcher developed by UCSC
ucsc
visualization
cancer
updated 11 months ago by
Ram
44k • written 8.7 years ago by
ivivek_ngs
★ 5.2k
1
vote
2
replies
5.5k
views
Tool:
TCGA & METABRIC Breast Cancer Subtype Survival Curve
gene
RNA-Seq
updated 11 months ago by
Ram
44k • written 6.9 years ago by
xushutan
▴ 40
19
votes
2
replies
5.4k
views
Tool:
CIViC - Clinical Interpretation of Variants in Cancer
clinical-interpretation
civic
variant
cancer
updated 11 months ago by
Ram
44k • written 9.2 years ago by
Obi Griffith
20k
26
votes
4
replies
5.3k
views
Tool:
Dgidb - Mining The Druggable Genome
dgidb
drug-gene-interaction
updated 11 months ago by
Ram
44k • written 10.6 years ago by
Obi Griffith
20k
7
votes
0
replies
5.3k
views
Tool:
Gem: Genome Wide Event Finding And Motif Discovery
motif
updated 11 months ago by
Ram
44k • written 11.5 years ago by
Ian
6.0k
11
votes
2
replies
5.3k
views
Tool:
ChIPQC: a package for assessing quality of ChIP-seq samples and experiments
quality-control
quality-assessment
ChIP-Seq
updated 11 months ago by
Ram
44k • written 10.1 years ago by
Rory Stark
★ 2.0k
5
votes
4
replies
5.3k
views
Tool:
Contiguator: A Bacterial Genomes Finishing Tool For Structural Insights On Draft Genomes
reference-genome
contigs
updated 11 months ago by
Ram
44k • written 11.9 years ago by
mgalactus
▴ 770
13
votes
6
replies
5.2k
views
Tool:
csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV
Golang
TSV
9 months ago by
shenwei356
8.5k
2
votes
6
replies
5.2k
views
Tool:
Variantannotation Package (Bioconductor)
snp
variant-annotation
updated 11 months ago by
Ram
44k • written 11.8 years ago by
Malachi Griffith
20k
56
votes
23
replies
5.2k
views
10 follow
Tool:
ASCIIGenome: Text Only Genome Viewer!
terminal
genome-browser
java
ASCIIGenome
updated 11 months ago by
Ram
44k • written 7.9 years ago by
dariober
14k
515 results • Page
2 of 11
Recent Votes
Answer: Allele count of 2 for homoplasmic MT variants in VCF
Find count of reads in BAM file that fall within BED region
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
C: Reads mapped to another chromosome in paired-end data of RNA-seq
How to classify cells based on the expression of genes in scRNA-seq
Answer: Using GATK MarkDuplicates for targeted sequencing data
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Recent Replies
Comment: Flag multiple filtering steps on VCF files using VEP
by
Pierre Lindenbaum
162k
I don't understand that question.
Comment: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> But your answer is exactly the opposite of what I want oh I see. but i don't understand the logic why: "Ch1 200 250" and "Ch1 150 220" …
Comment: merge overlaps and remove non overlap genomic windows
by
reza
▴ 300
sorry i edited my example. But your answer is exactly the opposite of what I want
Answer: merge overlaps and remove non overlap genomic windows
by
Pierre Lindenbaum
162k
> have two bed files these are not bed files. A chromosome is missing in chromosome 1 > How can I create a file from the two mention…
Comment: Small secondary peak for per sequence GC content - FASTQC results (bulk RNA-seq)
by
GenoMax
142k
Have you checked for presence of rRNA in the affected samples? That can be one possibility for these peaks. In theory if you are aligning …
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
GenoMax
142k
Please accept the answer (green check mark) to provide closure to this thread.
Comment: Trimmomatic running but files containing purged reads are empty
by
GenoMax
142k
Perhaps there were no low quality reads either.
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
Arton
▴ 10
Thank you for the helpful answer!
Comment: How to get the ratio of allele counts from GATK derived VCF file?
by
DBScan
▴ 300
I think GATK only counts informative reads in AD, do you have a DP field? DP should be closer what FreeBayes reports. You can also check GA…
Comment: Multiplexing for pooled CRISPR screen sequencing
by
Tuấn Anh
• 0
Thank you GenoMax! So would we just prepare the dual-indexed library and ask the sequencing service to do single-end sequencing?
Answer: Construction of circos plot from WGS data
by
marco.barr
▴ 130
Hi Anitha, you can take inspiration from here on which data to use and how to set up your WGS circle plot. [https://www.tandfonline.com/…
Comment: Trimmomatic running but files containing purged reads are empty
by
Wilber0x
▴ 50
Thanks for the advice, it seems like it is likely I have the incorrect adaptor sequences, though I am still surprised that no low quality r…
Answer: Trimmomatic running but files containing purged reads are empty
by
GenoMax
142k
> Why is trimmomatic not removing any reads? It is not mandatory that your data have extraneous/adapter sequence. If no extraneous sequenc…
Comment: FastQC interpretation - 16S sequencing
by
GenoMax
142k
Since a specific region is being amplified it is expected that many of the library fragments will have identical sequences. Thus the low nu…
Comment: FastQC interpretation - 16S sequencing
by
Christopher
▴ 10
@genomax Thank you so much for replying. I was quite unsure about the qualities. One more question. There is no problem within nucleotide d…
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