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737 results • Page
2 of 15
Sort: Views
Rank
Views
Votes
Replies
19
votes
5
replies
9.0k
views
Tool:
Automatic IGV snapshot script
ChIP-Seq
IGV
updated 14 months ago by
Ram
44k • written 7.2 years ago by
steve
★ 3.5k
8
votes
9
replies
9.0k
views
Tool:
Lofreq: A Fast And Sensitive Variant-Caller For Inferring Single-Nucleotide Variants From Ngs Data
snp
next-gen
somatic-variant
updated 10 months ago by
Ram
44k • written 11.6 years ago by
Andreas
★ 2.5k
15
votes
19
replies
8.8k
views
6 follow
Tool:
Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations
vcf
database
genome
variation
updated 11 months ago by
Ram
44k • written 11.1 years ago by
Aaronquinlan
12k
6
votes
3
replies
8.8k
views
Tool:
Masc - A Tool For Calculating Mean Fragment Size For Chip-Seq Peak Calling Analysis
chip-seq
updated 11 months ago by
Ram
44k • written 11.3 years ago by
Ian
6.0k
16
votes
9
replies
8.7k
views
Tool:
Introducing eLabFTW : free open source electronic lab notebook
eln
open-source
notebook-software
updated 2.4 years ago by
Ram
44k • written 9.8 years ago by
Nico
▴ 190
22
votes
4
replies
8.6k
views
Tool:
Very Bad Things
python
text
updated 17 months ago by
Ram
44k • written 11.3 years ago by
brentp
24k
9
votes
1
reply
8.6k
views
Tool:
Rseqqc And Rna-Seqqc - Quality Control Software For Rna-Seq Data
rna-seq
qc
updated 10 months ago by
Ram
44k • written 11.7 years ago by
Istvan Albert
100k
22
votes
5
replies
8.4k
views
Tool:
Salmon: A fast and versatile new tool for RNA-seq quantification
RNA-Seq
updated 2.2 years ago by
Ram
44k • written 9.4 years ago by
Rob
6.6k
15
votes
11
replies
8.3k
views
Tool:
Arriba: Fast and accurate gene fusion detection from RNA-Seq data
variant-calling
RNA-Seq
cancer
gene-fusion
updated 11 months ago by
Ram
44k • written 6.3 years ago by
uhrigs
▴ 150
48
votes
24
replies
8.3k
views
14 follow
Tool:
Hera: A new tool for RNA-Seq analysis
kallisto
RNA-Seq
STAR
gene-fusion
updated 11 months ago by
Ram
44k • written 6.8 years ago by
sonpham
▴ 580
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
25
votes
19
replies
8.2k
views
10 follow
Tool:
pathfindR - Enrichment Analysis using Active Subnetworks
subnetwork
R
pathway-enrichment
updated 11 months ago by
Ram
44k • written 6.2 years ago by
egeulgen
★ 1.3k
4
votes
0
replies
8.2k
views
Tool:
Snprelate: A Toolset For Relatedness And Principal Component Analysis Of Snp Data
parallel
pca
r
updated 10 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 10 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 10 months ago by
Ram
44k • written 11.6 years ago by
brentp
24k
10
votes
2
replies
7.5k
views
Tool:
fastp, the ultra-fast FASTQ preprocessing tool, is now on BioConda
fastp
updated 14 months ago by
Ram
44k • written 6.4 years ago by
chen
★ 2.5k
13
votes
2
replies
7.4k
views
Tool:
Software For Detecting Differential Abundance In Meta-Genomic Samples
metagenomics
updated 10 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 10 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 10 months ago by
Ram
44k • written 10.7 years ago by
William
★ 5.3k
8
votes
10
replies
7.2k
views
7 follow
Tool:
Transcription Factor Binding Sites, Motifs and Expression Profiles from ~10200 ChIP-seq and ~20000 RNA-seq samples
ChIP-Seq
transcription-factor
miRNA
lncRNA
updated 13 months ago by
Ram
44k • written 7.6 years ago by
lsp03yjh
▴ 860
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 10 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 10 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 10 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 5.6 years ago by
sonpham
▴ 580
4
votes
2
replies
6.6k
views
Tool:
pdb-tools: a set of Python scripts to manipulate PDB files.
python
pdb
modeling
updated 23 months ago by
Ram
44k • written 9.1 years ago by
João Rodrigues
★ 2.5k
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
11
votes
14
replies
6.5k
views
6 follow
Tool:
[share] Script to bulk retrieve DNA sequences by protein IDs from GenBank
python
genbank
sequence
cds
protein
updated 2.3 years ago by
Ram
44k • written 9.5 years ago by
qiyunzhu
▴ 130
1
vote
0
replies
6.5k
views
Tool:
Free available Supercomputing services - List
Supercomputing
grid
Assembly
annotation
updated 23 months ago by
Ram
44k • written 9.1 years ago by
margxenscienculo
▴ 50
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 10 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
11
votes
7
replies
6.2k
views
Tool:
RNA Modification Database and Epitranscriptome Sequencing Data
Epitranscriptome
m5C
m6A
RNA-modification
m1A
updated 21 months ago by
Ram
44k • written 8.6 years ago by
lsp03yjh
▴ 860
2
votes
5
replies
6.1k
views
Tool:
umitools - working with UMI incorporated data
UMI
sequencing
updated 10 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 10 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
737 results • Page
2 of 15
Recent Votes
Answer: geom_bar issue in ggplot2 with xlim()
A: How Can I Get The Human Chromosome Centromere Position And Chromosome Length In
GO analysis: Different results EnrichGO vs ShinyGO
Comment: NGS forensics: how to know if data is fabricated
T2T-CHM13 "complete" human genome gff/gtf annotation file
Answer: T2T-CHM13 "complete" human genome gff/gtf annotation file
Comment: Problem in getting geo file through GEOQUERY
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Recent Awards •
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andres.firrincieli
3.6k
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▴ 150
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▴ 120
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Recent Replies
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Luqman
• 0
Yes please see below: TraesCS2B02G372900 TraesCS2B02G375100 TraesCS2B02G374700 TraesCS2B02G382000
Comment: Functional enrichment analysis for unique gene IDs
by
Pegasus
▴ 100
Thanks for your answer, but as far as I know, gProfiler2 does not support bacteria. Could you please suggest alternative websites or softwa…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Hi Alex, I'm sorry if I wasn't initially clear! The question hasn't changed; I had written in this post that I wanted all pairwise combinat…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
by
Nyksubuz
▴ 20
Could share some examples for gene_ids?
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
yeah but i am unable to find the link of GPL6244.soft.gz
Comment: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
> Can you send me ftp link so I can download that soft file manually? Please find this link on your own by browsing the respective GEO ent…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Thanks . I have downloaded all other files but just have problem in Error in downloadFile(myurl, destfile, mode = mode, quiet = TRUE)…
Answer: Problem in getting geo file through GEOQUERY
by
ATpoint
82k
Code runs for me and finishes in seconds. Maybe some poor internet connection on your end. Just set the timeout to 9999999 and retry. If th…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
ezz3
• 0
Thanks. I was wondering if that is the case but was having some issues understanding the transanno code which is written in rust and I don…
Answer: Multi-ploid data in ANGSD and NGSadmix
by
andersdetermig
▴ 20
1 ) I would not expect the haploid individuals to always cluster together but the model assumptions are violated. First of all the diploid…
Comment: transanno liftvcf "Error: length of chromosome [chr] is not equal to length in c
by
Pierre Lindenbaum
161k
"Are you using correct reference?" may be your reference is not using the same chrM. see https://www.biostars.org/p/199796/#199803
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
shpak.max
▴ 50
Could you please elaborate on what you mean by passing -L or -V, i.e. what would the appropriate argument be for -L with UnifiedGenotyper f…
Answer: Add stats to the plot
by
Ghada
• 0
It works. I have added this code my_comparisons=list(c("HRSV", "HRSV_RBV")) plot + stat_compare_means(method = "wilcox.test",…
Comment: Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
by
LChart
3.9k
I believe UnifiedGenotyper is a locus walker that sets `emitEmptySites() = False`. As such you will not see entries for positions that have…
Comment: Problem in getting geo file through GEOQUERY
by
anasjamshed
▴ 120
Basically this is my code: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # # pkgs <- rowna…
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