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733 results • Page 2 of 15
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22
votes
4
replies
8.6k
views
Tool: Very Bad Things
python text
updated 17 months ago by 43k • written 11.2 years ago by 24k
22
votes
22
replies
18k
views
Tool: Pan-Cancer Analysis And Networks Of LncRNAs, MiRNAs, circRNAs, CeRNAs And RNA-Binding Proteins From TCGA 32 Cancer Types and CLIP-seq data
cancer TCGA RNA-Binding-Proteins miRNA lncRNA
updated 19 months ago by 43k • written 10.2 years ago by ▴ 860
21
votes
14
replies
9.4k
views
Tool: trackplot: Fast and minimal dependency standalone R script to generate IGV style locus tracks from bigWig files
visualization igv ChIP-Seq R bigwigs
updated 10 months ago by 43k • written 3.4 years ago by ★ 3.2k
21
votes
11
replies
11k
views
Tool: Segemehl: A Fast One-Stop-Shop Mapping Tool
mapping next-gen
updated 10 months ago by 43k • written 11.6 years ago by 11k
21
votes
11
replies
2.8k
views
Tool: log / log.bio - keeping track of command line workflows
ac.gt log.bio log
updated 19 months ago by 43k • written 8.7 years ago by 13k
20
votes
23
replies
7.2k
views
6 follow
Tool: EaSeq - Interactive ChIP-seq analysis and visualization (for Windows)
easeq Windows Visualization ChIP-Seq
updated 10 months ago by 43k • written 8.1 years ago by ▴ 460
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 10 months ago by 43k • written 8.0 years ago by ★ 2.5k
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 43k • written 10.0 years ago by ▴ 670
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 10 months ago by 43k • written 11.1 years ago by ★ 1.7k
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 10 months ago by 43k • written 6.6 years ago by 47k
19
votes
2
replies
5.3k
views
Tool: CIViC - Clinical Interpretation of Variants in Cancer
clinical-interpretation civic variant cancer
updated 10 months ago by 43k • written 9.2 years ago by 20k
19
votes
5
replies
8.9k
views
Tool: Automatic IGV snapshot script
ChIP-Seq IGV
updated 13 months ago by 43k • written 7.2 years ago by ★ 3.5k
18
votes
1
reply
3.5k
views
Tool: Human NGS Cancer Data for tool development, algorithm benchmarking, teaching, pipeline evaluation, etc.
WGS Benchmarking Cancer-Data
updated 18 months ago by 43k • written 8.8 years ago by 19k
18
votes
21
replies
4.4k
views
Tool: uQ - small binary FASTQ
Compression FASTQ
updated 10 months ago by 43k • written 7.2 years ago by 13k
18
votes
2
replies
6.0k
views
Tool: vcfanno quickly annotate a vcf with other VCFs, BEDs, BAMs
VCF variant-annotation
updated 10 months ago by 43k • written 8.9 years ago by 24k
18
votes
22
replies
4.6k
views
Tool: FAST: FAST Analysis of Sequences Toolbox
NCBI-Taxonomy pipeline multiFASTA BioPerl
updated 22 months ago by 43k • written 9.1 years ago by ▴ 70
18
votes
39
replies
4.3k
views
Tool: CBioInfCpp.h as a C++ lib containing some functions for bioinformatics
cpp
updated 11 months ago by 43k • written 5.1 years ago by ▴ 50
18
votes
30
replies
10k
views
6 follow
Tool: Introducing FilterByTile: Remove Low-Quality Reads Without Adding Bias
Illumina BBMap filterbytile
updated 10 months ago by 43k • written 7.4 years ago by 20k
18
votes
6
replies
4.8k
views
Tool: R code for ecological data analysis
next-gen R Metagenomics
updated 2.1 years ago by 43k • written 9.3 years ago by ★ 1.8k
17
votes
11
replies
11k
views
6 follow
Tool: Pyfaidx: Efficient, "Pythonic" Random Access To Fasta Files Using Samtools-Compatible Indexing
fasta python samtools
updated 10 months ago by 43k • written 10.2 years ago by 10k
17
votes
25
replies
2.4k
views
Tool: Platform for Bioinformatics Students, Scholars and Scientists
sequence genome
updated 10 months ago by 43k • written 8.2 years ago by ▴ 50
17
votes
9
replies
6.1k
views
Tool: Pathomx: Metabolic Pathway Visualisation And Analysis
python pathway-visualization
updated 10 months ago by 43k • written 11.1 years ago by ▴ 180
17
votes
9
replies
17k
views
6 follow
Tool: ggrepel: repel overlapping text labels in ggplot2
R visualization
updated 10 months ago by 43k • written 8.3 years ago by ★ 2.3k
16
votes
16
replies
7.6k
views
6 follow
Tool: Oncofuse: Prediction Of Driver Gene Fusions From Ngs Data
annotation fusion rna-seq ngs
updated 10 months ago by 43k • written 10.7 years ago by 3.5k
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 43k • written 9.7 years ago by ▴ 190
16
votes
3
replies
11k
views
Tool: Vcflib Documentation
vcf
updated 10 months ago by 43k • written 11.1 years ago by ★ 2.4k
15
votes
9
replies
3.4k
views
Tool: FlexiDot: highly customizable, ambiguity-aware dotplots
dotplot visualization sequence-analysis
updated 10 months ago by 43k • written 6.0 years ago by ▴ 230
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 43k • written 10.6 years ago by ★ 5.3k
15
votes
8
replies
2.4k
views
Tool: One Stop Solution for NGS Data Analysis
Predefined Robust NGS Analysis Tool
8.0 years ago by Persistent LABS ▴ 750
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 10 months ago by 43k • written 6.2 years ago by ▴ 150
15
votes
19
replies
8.7k
views
6 follow
Tool: Gemini: Integrative Exploration Of Genetic Variation And Genome Annotations
vcf database genome variation
updated 10 months ago by 43k • written 11.0 years ago by 12k
15
votes
2
replies
3.1k
views
Tool: EnhancedVolcano becomes a pseudo-EnhancedMA
enhancedMA enhancedvolcano
updated 10 months ago by 43k • written 3.7 years ago by 87k
14
votes
4
replies
4.5k
views
Tool: Seq_File: C Library For Reading Multiple Bioinformatics Sequence File Formats
fasta fastq bam sam
updated 10 months ago by 43k • written 11.4 years ago by 22k
14
votes
4
replies
4.8k
views
Tool: Revolution (?) in CNA detection using exome/targeted sequencing
copy-number-alteration next-gen
updated 10 months ago by 43k • written 9.0 years ago by ★ 7.8k
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 10 months ago by 43k • written 7.8 years ago by ★ 2.6k
14
votes
3
replies
4.1k
views
Tool: Bedops V2.2 Released
bed
updated 10 months ago by 43k • written 11.0 years ago by 35k
13
votes
2
replies
7.4k
views
Tool: Software For Detecting Differential Abundance In Meta-Genomic Samples
metagenomics
updated 10 months ago by 43k • written 11.5 years ago by 100k
13
votes
1
reply
6.5k
views
Tool: clusterProfiler: an R package for comparing biological themes among gene clusters
GO clusterProfiler KEGG R GSEA
updated 10 months ago by 43k • written 7.8 years ago by ★ 2.6k
13
votes
0
replies
2.8k
views
Tool: Book: GNU Parallel 2018 - for beginners and advanced users
parallel ngs
updated 10 months ago by 43k • written 5.5 years ago by ★ 4.4k
13
votes
1
reply
3.7k
views
Tool: Script to compute the effective genome size: epic-effective
ChIP-Seq
updated 10 months ago by 43k • written 8.1 years ago by ▴ 960
13
votes
6
replies
4.8k
views
Tool: GAWN - Genome Annotation Without Nightmares
genome-annotation
updated 10 months ago by 43k • written 6.8 years ago by 11k
13
votes
1
reply
4.6k
views
Tool: sam2pairwise: a tool to visualize SAM entries as pairwise alignments
sam alignment
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 310
13
votes
8
replies
4.3k
views
Tool: MSigDB for Multiple Organisms in a Tidy Data Format
msigdb pathways R gsea
updated 10 months ago by 43k • written 6.1 years ago by 13k
13
votes
14
replies
6.1k
views
9 follow
Tool: open-cravat: variant annotation tool
open-cravat
updated 10 months ago by 43k • written 5.4 years ago by ▴ 260
13
votes
14
replies
2.3k
views
Tool: Collaboration on an empirical QC tool
RNA-Seq QC sequencing
updated 10 months ago by 43k • written 7.0 years ago by 54k
13
votes
25
replies
11k
views
9 follow
Tool: Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
analysis sequencing ngs
updated 10 months ago by 43k • written 10.8 years ago by 3.5k
13
votes
6
replies
3.0k
views
Tool: Open source bioinformatics tools: Blaster, Primer Factory, Labtools
primer blast alignment bowtie
updated 2.4 years ago by 43k • written 9.3 years ago by ▴ 110
13
votes
6
replies
5.2k
views
Tool: csvtk - a cross-platform, efficient, practical and pretty CSV/TSV toolkit
CSV Golang TSV
8 months ago by shenwei356 8.5k
13
votes
7
replies
9.7k
views
Tool: Command-Line Software For Bigwig Data
bigwig
updated 10 months ago by 43k • written 10.5 years ago by ▴ 90
13
votes
7
replies
4.2k
views
Tool: I-PV: a CIRCOS module for interactive protein sequence visualization
interactive javascript circos sequence
updated 20 months ago by 43k • written 8.5 years ago by ★ 1.2k
733 results • Page 2 of 15
Recent Votes
Answer: GRCh38.gmap file
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
A: PCA plot from read count matrix from RNA-Seq
A: PCA plot from read count matrix from RNA-Seq
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Recent Replies
Comment: Design matrix Differential expression analysis by Gordon Smyth ★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file by lorena9132 ▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file by Mathew ▴ 30
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data by Mathew ▴ 30
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis by SHN ▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx by vjanve • 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction by Expert ▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction by ATpoint 82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error by Ruqaiya • 0
This the tool still problematic?
Comment: Segmentation error while using a tool by Ruqaiya • 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool by Ruqaiya • 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool by Mensur Dlakic ★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool by Thanujay S • 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA by Thanujay S • 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool by Ruqaiya • 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
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